Mercurial > repos > fubar > differential_count_models
changeset 50:60aceade5350 draft
removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
| author | fubar |
|---|---|
| date | Mon, 23 Dec 2013 21:36:34 -0500 |
| parents | 89ed2d3c529f |
| children | ccc5a33bb358 |
| files | rgToolFactory.py rgedgeRpaired_nocamera.xml test-data/edgeRtest1out.html test-data/edgeRtest1out.xls test-data/gentestdata.sh test-data/test_bams2mx.xls tool_dependencies.xml |
| diffstat | 7 files changed, 6906 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgToolFactory.py Mon Dec 23 21:36:34 2013 -0500 @@ -0,0 +1,634 @@ +# rgToolFactory.py +# see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home +# +# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012 +# +# all rights reserved +# Licensed under the LGPL +# suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home +# +# august 2013 +# found a problem with GS if $TMP or $TEMP missing - now inject /tmp and warn +# +# july 2013 +# added ability to combine images and individual log files into html output +# Needs proper yaml control file but for now for each section you want separated out in the +# HTML page, you need to use a name like foo or bar or header - they will be presented in alphabetic order +# +# Iff there's a log file foo.log and it will be layed out as preformated text in the HTML output +# together with all images named like "foo_*.pdf in a separate "foo" section of the document +# otherwise old format for html +# +# January 2013 +# problem pointed out by Carlos Borroto +# added escaping for <>$ - thought I did that ages ago... +# +# August 11 2012 +# changed to use shell=False and cl as a sequence + +# This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye. +# It also serves as the wrapper for the new tool. +# +# you paste and run your script +# Only works for simple scripts that read one input from the history. +# Optionally can write one new history dataset, +# and optionally collect any number of outputs into links on an autogenerated HTML page. + +# DO NOT install on a public or important site - please. + +# installed generated tools are fine if the script is safe. +# They just run normally and their user cannot do anything unusually insecure +# but please, practice safe toolshed. +# Read the fucking code before you install any tool +# especially this one + +# After you get the script working on some test data, you can +# optionally generate a toolshed compatible gzip file +# containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for +# safe and largely automated installation in a production Galaxy. + +# If you opt for an HTML output, you get all the script outputs arranged +# as a single Html history item - all output files are linked, thumbnails for all the pdfs. +# Ugly but really inexpensive. +# +# Patches appreciated please. +# +# +# long route to June 2012 product +# Behold the awesome power of Galaxy and the toolshed with the tool factory to bind them +# derived from an integrated script model +# called rgBaseScriptWrapper.py +# Note to the unwary: +# This tool allows arbitrary scripting on your Galaxy as the Galaxy user +# There is nothing stopping a malicious user doing whatever they choose +# Extremely dangerous!! +# Totally insecure. So, trusted users only +# +# preferred model is a developer using their throw away workstation instance - ie a private site. +# no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool. +# + +import sys +import shutil +import subprocess +import os +import time +import tempfile +import optparse +import tarfile +import re +import shutil +import math + +progname = os.path.split(sys.argv[0])[1] +myversion = 'V000.2 June 2012' +verbose = False +debug = False +toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory' + +def timenow(): + """return current time as a string + """ + return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) + +html_escape_table = { + "&": "&", + ">": ">", + "<": "<", + "$": "\$" + } + +def html_escape(text): + """Produce entities within text.""" + return "".join(html_escape_table.get(c,c) for c in text) + +def cmd_exists(cmd): + return subprocess.call("type " + cmd, shell=True, + stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0 + + +class ScriptRunner: + """class is a wrapper for an arbitrary script + """ + + def __init__(self,opts=None,treatbashSpecial=True): + """ + cleanup inputs, setup some outputs + + """ + self.useGM = cmd_exists('gm') + self.useIM = cmd_exists('convert') + self.useGS = cmd_exists('gs') + self.temp_warned = False # we want only one warning if $TMP not set + self.treatbashSpecial = treatbashSpecial + if opts.output_dir: # simplify for the tool tarball + os.chdir(opts.output_dir) + self.thumbformat = 'png' + self.opts = opts + self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but.. + self.toolid = self.toolname + self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later + self.pyfile = self.myname # crude but efficient - the cruft won't hurt much + self.xmlfile = '%s.xml' % self.toolname + s = open(self.opts.script_path,'r').readlines() + s = [x.rstrip() for x in s] # remove pesky dos line endings if needed + self.script = '\n'.join(s) + fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter)) + tscript = open(self.sfile,'w') # use self.sfile as script source for Popen + tscript.write(self.script) + tscript.close() + self.indentedScript = '\n'.join([' %s' % x for x in s]) # for restructured text in help + self.escapedScript = '\n'.join([html_escape(x) for x in s]) + self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.toolname) + if opts.output_dir: # may not want these complexities + self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname) + art = '%s.%s' % (self.toolname,opts.interpreter) + artpath = os.path.join(self.opts.output_dir,art) # need full path + artifact = open(artpath,'w') # use self.sfile as script source for Popen + artifact.write(self.script) + artifact.close() + self.cl = [] + self.html = [] + a = self.cl.append + a(opts.interpreter) + if self.treatbashSpecial and opts.interpreter in ['bash','sh']: + a(self.sfile) + else: + a('-') # stdin + a(opts.input_tab) + a(opts.output_tab) + self.outFormats = 'tabular' # TODO make this an option at tool generation time + self.inputFormats = 'tabular' # TODO make this an option at tool generation time + self.test1Input = '%s_test1_input.xls' % self.toolname + self.test1Output = '%s_test1_output.xls' % self.toolname + self.test1HTML = '%s_test1_output.html' % self.toolname + + def makeXML(self): + """ + Create a Galaxy xml tool wrapper for the new script as a string to write out + fixme - use templating or something less fugly than this example of what we produce + + <tool id="reverse" name="reverse" version="0.01"> + <description>a tabular file</description> + <command interpreter="python"> + reverse.py --script_path "$runMe" --interpreter "python" + --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file" + </command> + <inputs> + <param name="input1" type="data" format="tabular" label="Select a suitable input file from your history"/><param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/> + + </inputs> + <outputs> + <data format="tabular" name="tab_file" label="${job_name}"/> + + </outputs> + <help> + +**What it Does** + +Reverse the columns in a tabular file + + </help> + <configfiles> + <configfile name="runMe"> + +# reverse order of columns in a tabular file +import sys +inp = sys.argv[1] +outp = sys.argv[2] +i = open(inp,'r') +o = open(outp,'w') +for row in i: + rs = row.rstrip().split('\t') + rs.reverse() + o.write('\t'.join(rs)) + o.write('\n') +i.close() +o.close() + + + </configfile> + </configfiles> + </tool> + + """ + newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s"> + %(tooldesc)s + %(command)s + <inputs> + %(inputs)s + </inputs> + <outputs> + %(outputs)s + </outputs> + <configfiles> + <configfile name="runMe"> + %(script)s + </configfile> + </configfiles> + %(tooltests)s + <help> + %(help)s + </help> + </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto + + newCommand="""<command interpreter="python"> + %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s" + --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s + </command>""" # may NOT be an input or htmlout + tooltestsTabOnly = """<tests><test> + <param name="input1" value="%(test1Input)s" ftype="tabular"/> + <param name="job_name" value="test1"/> + <param name="runMe" value="$runMe"/> + <output name="tab_file" file="%(test1Output)s" ftype="tabular"/> + </test></tests>""" + tooltestsHTMLOnly = """<tests><test> + <param name="input1" value="%(test1Input)s" ftype="tabular"/> + <param name="job_name" value="test1"/> + <param name="runMe" value="$runMe"/> + <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/> + </test></tests>""" + tooltestsBoth = """<tests><test> + <param name="input1" value="%(test1Input)s" ftype="tabular"/> + <param name="job_name" value="test1"/> + <param name="runMe" value="$runMe"/> + <output name="tab_file" file="%(test1Output)s" ftype="tabular" /> + <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/> + </test></tests>""" + xdict = {} + xdict['tool_version'] = self.opts.tool_version + xdict['test1Input'] = self.test1Input + xdict['test1HTML'] = self.test1HTML + xdict['test1Output'] = self.test1Output + if self.opts.make_HTML and self.opts.output_tab <> 'None': + xdict['tooltests'] = tooltestsBoth % xdict + elif self.opts.make_HTML: + xdict['tooltests'] = tooltestsHTMLOnly % xdict + else: + xdict['tooltests'] = tooltestsTabOnly % xdict + xdict['script'] = self.escapedScript + # configfile is least painful way to embed script to avoid external dependencies + # but requires escaping of <, > and $ to avoid Mako parsing + if self.opts.help_text: + xdict['help'] = open(self.opts.help_text,'r').read() + else: + xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation' + coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::'] + coda.append(self.indentedScript) + coda.append('**Attribution** This Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.' % (self.opts.user_email,timenow())) + coda.append('See %s for details of that project' % (toolFactoryURL)) + coda.append('Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. ') + coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573') + xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda)) + if self.opts.tool_desc: + xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc + else: + xdict['tooldesc'] = '' + xdict['command_outputs'] = '' + xdict['outputs'] = '' + if self.opts.input_tab <> 'None': + xdict['command_inputs'] = '--input_tab "$input1" ' # the space may matter a lot if we append something + xdict['inputs'] = '<param name="input1" type="data" format="%s" label="Select a suitable input file from your history"/> \n' % self.inputFormats + else: + xdict['command_inputs'] = '' # assume no input - eg a random data generator + xdict['inputs'] = '' + xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname + xdict['toolname'] = self.toolname + xdict['toolid'] = self.toolid + xdict['interpreter'] = self.opts.interpreter + xdict['scriptname'] = self.sfile + if self.opts.make_HTML: + xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" ' + xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n' + if self.opts.output_tab <> 'None': + xdict['command_outputs'] += ' --output_tab "$tab_file"' + xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats + xdict['command'] = newCommand % xdict + xmls = newXML % xdict + xf = open(self.xmlfile,'w') + xf.write(xmls) + xf.write('\n') + xf.close() + # ready for the tarball + + + def makeTooltar(self): + """ + a tool is a gz tarball with eg + /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ... + """ + retval = self.run() + if retval: + print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry' + sys.exit(1) + self.makeXML() + tdir = self.toolname + os.mkdir(tdir) + if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe.. + testdir = os.path.join(tdir,'test-data') + os.mkdir(testdir) # make tests directory + shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input)) + if self.opts.output_tab <> 'None': + shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output)) + if self.opts.make_HTML: + shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML)) + if self.opts.output_dir: + shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log')) + op = '%s.py' % self.toolname # new name + outpiname = os.path.join(tdir,op) # path for the tool tarball + pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM) + notes = ['# %s - a self annotated version of %s generated by running %s\n' % (op,pyin,pyin),] + notes.append('# to make a new Galaxy tool called %s\n' % self.toolname) + notes.append('# User %s at %s\n' % (self.opts.user_email,timenow())) + pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm + notes += pi + outpi = open(outpiname,'w') + outpi.write(''.join(notes)) + outpi.write('\n') + outpi.close() + stname = os.path.join(tdir,self.sfile) + if not os.path.exists(stname): + shutil.copyfile(self.sfile, stname) + xtname = os.path.join(tdir,self.xmlfile) + if not os.path.exists(xtname): + shutil.copyfile(self.xmlfile,xtname) + tarpath = "%s.gz" % self.toolname + tar = tarfile.open(tarpath, "w:gz") + tar.add(tdir,arcname=self.toolname) + tar.close() + shutil.copyfile(tarpath,self.opts.new_tool) + shutil.rmtree(tdir) + ## TODO: replace with optional direct upload to local toolshed? + return retval + + + def compressPDF(self,inpdf=None,thumbformat='png'): + """need absolute path to pdf + note that GS gets confoozled if no $TMP or $TEMP + so we set it + """ + assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName) + our_env = os.environ.copy() + if not (our_env.get('TMP',None) or our_env.get('TEMP',None)): + our_env['TMP'] = '/tmp' + if not self.temp_warned: + print >> sys.stdout,'## WARNING - no $TMP or $TEMP!!! Please fix - using /tmp temporarily' + self.temp_warned = True + hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf)) + sto = open(hlog,'w') + outpdf = '%s_compressed' % inpdf + cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf] + x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env) + retval1 = x.wait() + sto.close() + if retval1 == 0: + os.unlink(inpdf) + shutil.move(outpdf,inpdf) + os.unlink(hlog) + else: + x = open(hlog,'r').readlines() + print >> sys.stdout,x + hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf)) + sto = open(hlog,'w') + outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat) + if self.useGM: + cl2 = ['gm', 'convert', inpdf, outpng] + else: # assume imagemagick + cl2 = ['convert', inpdf, outpng] + x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env) + retval2 = x.wait() + sto.close() + if retval2 <> 0: + x = open(hlog,'r').readlines() + print >> sys.stdout,x + else: + os.unlink(hlog) + retval = retval1 or retval2 + return retval + + + def getfSize(self,fpath,outpath): + """ + format a nice file size string + """ + size = '' + fp = os.path.join(outpath,fpath) + if os.path.isfile(fp): + size = '0 B' + n = float(os.path.getsize(fp)) + if n > 2**20: + size = '%1.1f MB' % (n/2**20) + elif n > 2**10: + size = '%1.1f KB' % (n/2**10) + elif n > 0: + size = '%d B' % (int(n)) + return size + + def makeHtml(self): + """ Create an HTML file content to list all the artifacts found in the output_dir + """ + + galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> + <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> + <title></title> + <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> + </head> + <body> + <div class="toolFormBody"> + """ + galhtmlattr = """<hr/><div class="infomessage">This tool (%s) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/>""" + galhtmlpostfix = """</div></body></html>\n""" + + flist = os.listdir(self.opts.output_dir) + flist = [x for x in flist if x <> 'Rplots.pdf'] + flist.sort() + html = [] + html.append(galhtmlprefix % progname) + html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow())) + fhtml = [] + if len(flist) > 0: + logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections + logfiles.sort() + logfiles = [x for x in logfiles if os.path.abspath(x) <> os.path.abspath(self.tlog)] + logfiles.append(os.path.abspath(self.tlog)) # make it the last one + pdflist = [] + npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf']) + for rownum,fname in enumerate(flist): + dname,e = os.path.splitext(fname) + sfsize = self.getfSize(fname,self.opts.output_dir) + if e.lower() == '.pdf' : # compress and make a thumbnail + thumb = '%s.%s' % (dname,self.thumbformat) + pdff = os.path.join(self.opts.output_dir,fname) + retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat) + if retval == 0: + pdflist.append((fname,thumb)) + else: + pdflist.append((fname,fname)) + if (rownum+1) % 2 == 0: + fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize)) + else: + fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize)) + for logfname in logfiles: # expect at least tlog - if more + if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later + sectionname = 'All tool run' + if (len(logfiles) > 1): + sectionname = 'Other' + ourpdfs = pdflist + else: + realname = os.path.basename(logfname) + sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log + ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname] + pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove + nacross = 1 + npdf = len(ourpdfs) + + if npdf > 0: + nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2))) + if int(nacross)**2 != npdf: + nacross += 1 + nacross = int(nacross) + width = min(400,int(1200/nacross)) + html.append('<H2>%s images and outputs</H2>' % sectionname) + html.append('<div class="toolFormTitle">Click on a thumbnail image to download the corresponding original PDF image</div>') + ntogo = nacross # counter for table row padding with empty cells + html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>') + for i,paths in enumerate(ourpdfs): + fname,thumb = paths + s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d" + alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname) + if ((i+1) % nacross == 0): + s += '</tr>\n' + ntogo = 0 + if i < (npdf - 1): # more to come + s += '<tr>' + ntogo = nacross + else: + ntogo -= 1 + html.append(s) + if html[-1].strip().endswith('</tr>'): + html.append('</table></div>\n') + else: + if ntogo > 0: # pad + html.append('<td> </td>'*ntogo) + html.append('</tr></table></div>\n') + logt = open(logfname,'r').readlines() + logtext = [x for x in logt if x.strip() > ''] + html.append('<H2>%s log output</H2>' % sectionname) + if len(logtext) > 1: + html.append('\n<pre>\n') + html += logtext + html.append('\n</pre>\n') + else: + html.append('%s is empty<br/>' % logfname) + if len(fhtml) > 0: + fhtml.insert(0,'<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n') + fhtml.append('</table></div><br/>') + html.append('<div class="toolFormTitle">All output files available for downloading</div>\n') + html += fhtml # add all non-pdf files to the end of the display + else: + html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter) + html.append(galhtmlpostfix) + htmlf = file(self.opts.output_html,'w') + htmlf.write('\n'.join(html)) + htmlf.write('\n') + htmlf.close() + self.html = html + + + def run(self): + """ + scripts must be small enough not to fill the pipe! + """ + if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']: + retval = self.runBash() + else: + if self.opts.output_dir: + ste = open(self.elog,'w') + sto = open(self.tlog,'w') + sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl)) + sto.flush() + p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,stdin=subprocess.PIPE,cwd=self.opts.output_dir) + else: + p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE) + p.stdin.write(self.script) + p.stdin.close() + retval = p.wait() + if self.opts.output_dir: + sto.close() + ste.close() + err = open(self.elog,'r').readlines() + if retval <> 0 and err: # problem + print >> sys.stderr,err + if self.opts.make_HTML: + self.makeHtml() + return retval + + def runBash(self): + """ + cannot use - for bash so use self.sfile + """ + if self.opts.output_dir: + s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl) + sto = open(self.tlog,'w') + sto.write(s) + sto.flush() + p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir) + else: + p = subprocess.Popen(self.cl,shell=False) + retval = p.wait() + if self.opts.output_dir: + sto.close() + if self.opts.make_HTML: + self.makeHtml() + return retval + + +def main(): + u = """ + This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as: + <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript" + </command> + """ + op = optparse.OptionParser() + a = op.add_option + a('--script_path',default=None) + a('--tool_name',default=None) + a('--interpreter',default=None) + a('--output_dir',default=None) + a('--output_html',default=None) + a('--input_tab',default="None") + a('--output_tab',default="None") + a('--user_email',default='Unknown') + a('--bad_user',default=None) + a('--make_Tool',default=None) + a('--make_HTML',default=None) + a('--help_text',default=None) + a('--tool_desc',default=None) + a('--new_tool',default=None) + a('--tool_version',default=None) + opts, args = op.parse_args() + assert not opts.bad_user,'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to admin_users in universe_wsgi.ini' % (opts.bad_user,opts.bad_user) + assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq' + assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript' + assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R' + if opts.output_dir: + try: + os.makedirs(opts.output_dir) + except: + pass + r = ScriptRunner(opts) + if opts.make_Tool: + retcode = r.makeTooltar() + else: + retcode = r.run() + os.unlink(r.sfile) + if retcode: + sys.exit(retcode) # indicate failure to job runner + + +if __name__ == "__main__": + main() + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgedgeRpaired_nocamera.xml Mon Dec 23 21:36:34 2013 -0500 @@ -0,0 +1,1095 @@ +<tool id="rgDifferentialCount" name="Differential_Count" version="0.23"> + <description>models using BioConductor packages</description> + <requirements> + <requirement type="package" version="3.11.11">atlas</requirement> + <requirement type="package" version="3.0.1">r3</requirement> + <requirement type="package" version="1.3.18">graphicsmagick</requirement> + <requirement type="package" version="9.07">ghostscript</requirement> + <requirement type="package" version="2.12">biocbasics</requirement> + </requirements> + + <command interpreter="python"> + rgToolFactory.py --script_path "$runme" --interpreter "Rscript" --tool_name "DifferentialCounts" + --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" + </command> + <inputs> + <param name="input1" type="data" format="tabular" label="Select an input matrix - rows are contigs, columns are counts for each sample" + help="Use the HTSeq based count matrix preparation tool to create these matrices from BAM/SAM files and a GTF file of genomic features"/> + <param name="title" type="text" value="Differential Counts" size="80" label="Title for job outputs" + help="Supply a meaningful name here to remind you what the outputs contain"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value="_" /> </valid> + </sanitizer> + </param> + <param name="treatment_name" type="text" value="Treatment" size="50" label="Treatment Name"/> + <param name="Treat_cols" label="Select columns containing treatment." type="data_column" data_ref="input1" numerical="True" + multiple="true" use_header_names="true" size="120" display="checkboxes"> + <validator type="no_options" message="Please select at least one column."/> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value="_" /> </valid> + </sanitizer> + </param> + <param name="control_name" type="text" value="Control" size="50" label="Control Name"/> + <param name="Control_cols" label="Select columns containing control." type="data_column" data_ref="input1" numerical="True" + multiple="true" use_header_names="true" size="120" display="checkboxes" optional="true"> + <validator type="no_options" message="Please select at least one column."/> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value="_" /> </valid> + </sanitizer> <validator type="no_options" message="Please select at least one column."/> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value="_" /> </valid> + </sanitizer> + + </param> + <param name="subjectids" type="text" optional="true" size="120" value = "" + label="IF SUBJECTS NOT ALL INDEPENDENT! Enter comma separated strings to indicate sample labels for (eg) pairing - must be one for every column in input" + help="Leave blank if no pairing, but eg if data from sample id A99 is in columns 2,4 and id C21 is in 3,5 then enter 'A99,C21,A99,C21'"> + <sanitizer> + <valid initial="string.letters,string.digits"><add value="," /> </valid> + </sanitizer> + </param> + <param name="fQ" type="float" value="0.3" size="5" label="Non-differential contig count quantile threshold - zero to analyze all non-zero read count contigs" + help="May be a good or a bad idea depending on the biology and the question. EG 0.3 = sparsest 30% of contigs with at least one read are removed before analysis"/> + <param name="useNDF" type="boolean" truevalue="T" falsevalue="F" checked="false" size="1" + label="Non differential filter - remove contigs below a threshold (1 per million) for half or more samples" + help="May be a good or a bad idea depending on the biology and the question. This was the old default. Quantile based is available as an alternative"/> + + <conditional name="edgeR"> + <param name="doedgeR" type="select" + label="Run this model using edgeR" + help="edgeR uses a negative binomial model and seems to be powerful, even with few replicates"> + <option value="F">Do not run edgeR</option> + <option value="T" selected="true">Run edgeR</option> + </param> + <when value="T"> + <param name="edgeR_priordf" type="integer" value="20" size="3" + label="prior.df for tagwise dispersion - lower value = more emphasis on each tag's variance. Replaces prior.n and prior.df = prior.n * residual.df" + help="0 = Use edgeR default. Use a small value to 'smooth' small samples. See edgeR docs and note below"/> + </when> + <when value="F"></when> + </conditional> + <conditional name="DESeq2"> + <param name="doDESeq2" type="select" + label="Run the same model with DESeq2 and compare findings" + help="DESeq2 is an update to the DESeq package. It uses different assumptions and methods to edgeR"> + <option value="F" selected="true">Do not run DESeq2</option> + <option value="T">Run DESeq2</option> + </param> + <when value="T"> + <param name="DESeq_fitType" type="select"> + <option value="parametric" selected="true">Parametric (default) fit for dispersions</option> + <option value="local">Local fit - this will automagically be used if parametric fit fails</option> + <option value="mean">Mean dispersion fit- use this if you really understand what you're doing - read the fine manual linked below in the documentation</option> + </param> + </when> + <when value="F"> </when> + </conditional> + <param name="doVoom" type="select" + label="Run the same model with Voom/limma and compare findings" + help="Voom uses counts per million and a precise transformation of variance so count data can be analysed using limma"> + <option value="F" selected="true">Do not run VOOM</option> + <option value="T">Run VOOM</option> + </param> + <!-- + <conditional name="camera"> + <param name="doCamera" type="select" label="Run the edgeR implementation of Camera GSEA for up/down gene sets" + help="If yes, you can choose a set of genesets to test and/or supply a gmt format geneset collection from your history"> + <option value="F" selected="true">Do not run GSEA tests with the Camera algorithm</option> + <option value="T">Run GSEA tests with the Camera algorithm</option> + </param> + <when value="T"> + <conditional name="gmtSource"> + <param name="refgmtSource" type="select" + label="Use a gene set (.gmt) from your history and/or use a built-in (MSigDB etc) gene set"> + <option value="indexed" selected="true">Use a built-in gene set</option> + <option value="history">Use a gene set from my history</option> + <option value="both">Add a gene set from my history to a built in gene set</option> + </param> + <when value="indexed"> + <param name="builtinGMT" type="select" label="Select a gene set matrix (.gmt) file to use for the analysis"> + <options from_data_table="gseaGMT_3.1"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No GMT v3.1 files are available - please install them"/> + </options> + </param> + </when> + <when value="history"> + <param name="ownGMT" type="data" format="gmt" label="Select a Gene Set from your history" /> + </when> + <when value="both"> + <param name="ownGMT" type="data" format="gseagmt" label="Select a Gene Set from your history" /> + <param name="builtinGMT" type="select" label="Select a gene set matrix (.gmt) file to use for the analysis"> + <options from_data_table="gseaGMT_4"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No GMT v4 files are available - please fix tool_data_table and loc files"/> + </options> + </param> + </when> + </conditional> + </when> + <when value="F"> + </when> + </conditional> + --> + <param name="fdrthresh" type="float" value="0.05" size="5" label="P value threshold for FDR filtering for amily wise error rate control" + help="Conventional default value of 0.05 recommended"/> + <param name="fdrtype" type="select" label="FDR (Type II error) control method" + help="Use fdr or bh typically to control for the number of tests in a reliable way"> + <option value="fdr" selected="true">fdr</option> + <option value="BH">Benjamini Hochberg</option> + <option value="BY">Benjamini Yukateli</option> + <option value="bonferroni">Bonferroni</option> + <option value="hochberg">Hochberg</option> + <option value="holm">Holm</option> + <option value="hommel">Hommel</option> + <option value="none">no control for multiple tests</option> + </param> + </inputs> + <outputs> + <data format="tabular" name="out_edgeR" label="${title}_topTable_edgeR.xls"> + <filter>edgeR['doedgeR'] == "T"</filter> + </data> + <data format="tabular" name="out_DESeq2" label="${title}_topTable_DESeq2.xls"> + <filter>DESeq2['doDESeq2'] == "T"</filter> + </data> + <data format="tabular" name="out_VOOM" label="${title}_topTable_VOOM.xls"> + <filter>doVoom == "T"</filter> + </data> + <data format="html" name="html_file" label="${title}.html"/> + </outputs> + <stdio> + <exit_code range="4" level="fatal" description="Number of subject ids must match total number of samples in the input matrix" /> + </stdio> + <tests> +<test> +<param name='input1' value='test_bams2mx.xls' ftype='tabular' /> + <param name='treatment_name' value='liver' /> + <param name='title' value='edgeRtest' /> + <param name='useNDF' value='' /> + <param name='doedgeR' value='T' /> + <param name='doVoom' value='T' /> + <param name='doDESeq2' value='T' /> + <param name='fdrtype' value='fdr' /> + <param name='edgeR_priordf' value="8" /> + <param name='fdrthresh' value="0.05" /> + <param name='control_name' value='heart' /> + <param name='subjectids' value='' /> + <param name='Control_cols' value='3,4,5,9' /> + <param name='Treat_cols' value='2,6,7,8' /> + <output name='out_edgeR' file='edgeRtest1out.xls' compare='diff' /> + <output name='html_file' file='edgeRtest1out.html' compare='diff' lines_diff='20' /> +</test> +</tests> + +<configfiles> +<configfile name="runme"> +<![CDATA[ +# +# edgeR.Rscript +# updated npv 2011 for R 2.14.0 and edgeR 2.4.0 by ross +# Performs DGE on a count table containing n replicates of two conditions +# +# Parameters +# +# 1 - Output Dir + +# Original edgeR code by: S.Lunke and A.Kaspi +reallybig = log10(.Machine\$double.xmax) +reallysmall = log10(.Machine\$double.xmin) +library('stringr') +library('gplots') +library('edgeR') +hmap2 = function(cmat,nsamp=100,outpdfname='heatmap2.pdf', TName='Treatment',group=NA,myTitle='title goes here') +{ +# Perform clustering for significant pvalues after controlling FWER + samples = colnames(cmat) + gu = unique(group) + gn = rownames(cmat) + if (length(gu) == 2) { + col.map = function(g) {if (g==gu[1]) "#FF0000" else "#0000FF"} + pcols = unlist(lapply(group,col.map)) + } else { + colours = rainbow(length(gu),start=0,end=4/6) + pcols = colours[match(group,gu)] } + dm = cmat[(! is.na(gn)),] + # remove unlabelled hm rows + nprobes = nrow(dm) + # sub = paste('Showing',nprobes,'contigs ranked for evidence of differential abundance') + if (nprobes > nsamp) { + dm =dm[1:nsamp,] + #sub = paste('Showing',nsamp,'contigs ranked for evidence for differential abundance out of',nprobes,'total') + } + newcolnames = substr(colnames(dm),1,20) + colnames(dm) = newcolnames + pdf(outpdfname) + heatmap.2(dm,main=myTitle,ColSideColors=pcols,col=topo.colors(100),dendrogram="col",key=T,density.info='none', + Rowv=F,scale='row',trace='none',margins=c(8,8),cexRow=0.4,cexCol=0.5) + dev.off() +} + +hmap = function(cmat,nmeans=4,outpdfname="heatMap.pdf",nsamp=250,TName='Treatment',group=NA,myTitle="Title goes here") +{ + # for 2 groups only was + #col.map = function(g) {if (g==TName) "#FF0000" else "#0000FF"} + #pcols = unlist(lapply(group,col.map)) + gu = unique(group) + colours = rainbow(length(gu),start=0.3,end=0.6) + pcols = colours[match(group,gu)] + nrows = nrow(cmat) + mtitle = paste(myTitle,'Heatmap: n contigs =',nrows) + if (nrows > nsamp) { + cmat = cmat[c(1:nsamp),] + mtitle = paste('Heatmap: Top ',nsamp,' DE contigs (of ',nrows,')',sep='') + } + newcolnames = substr(colnames(cmat),1,20) + colnames(cmat) = newcolnames + pdf(outpdfname) + heatmap(cmat,scale='row',main=mtitle,cexRow=0.3,cexCol=0.4,Rowv=NA,ColSideColors=pcols) + dev.off() +} + +qqPlot = function(descr='qqplot',pvector, outpdf='qqplot.pdf',...) +# stolen from https://gist.github.com/703512 +{ + o = -log10(sort(pvector,decreasing=F)) + e = -log10( 1:length(o)/length(o) ) + o[o==-Inf] = reallysmall + o[o==Inf] = reallybig + maint = descr + pdf(outpdf) + plot(e,o,pch=19,cex=1, main=maint, ..., + xlab=expression(Expected~~-log[10](italic(p))), + ylab=expression(Observed~~-log[10](italic(p))), + xlim=c(0,max(e)), ylim=c(0,max(o))) + lines(e,e,col="red") + grid(col = "lightgray", lty = "dotted") + dev.off() +} + +smearPlot = function(DGEList,deTags, outSmear, outMain) + { + pdf(outSmear) + plotSmear(DGEList,de.tags=deTags,main=outMain) + grid(col="lightgray", lty="dotted") + dev.off() + } + +boxPlot = function(rawrs,cleanrs,maint,myTitle,pdfname) +{ # + nc = ncol(rawrs) + #### for (i in c(1:nc)) {rawrs[(rawrs[,i] < 0),i] = NA} + fullnames = colnames(rawrs) + newcolnames = substr(colnames(rawrs),1,20) + colnames(rawrs) = newcolnames + newcolnames = substr(colnames(cleanrs),1,20) + colnames(cleanrs) = newcolnames + defpar = par(no.readonly=T) + print.noquote('raw contig counts by sample:') + print.noquote(summary(rawrs)) + print.noquote('normalised contig counts by sample:') + print.noquote(summary(cleanrs)) + pdf(pdfname) + par(mfrow=c(1,2)) + boxplot(rawrs,varwidth=T,notch=T,ylab='log contig count',col="maroon",las=3,cex.axis=0.35,main=paste('Raw:',maint)) + grid(col="lightgray",lty="dotted") + boxplot(cleanrs,varwidth=T,notch=T,ylab='log contig count',col="maroon",las=3,cex.axis=0.35,main=paste('After ',maint)) + grid(col="lightgray",lty="dotted") + dev.off() + pdfname = "sample_counts_histogram.pdf" + nc = ncol(rawrs) + print.noquote(paste('Using ncol rawrs=',nc)) + ncroot = round(sqrt(nc)) + if (ncroot*ncroot < nc) { ncroot = ncroot + 1 } + m = c() + for (i in c(1:nc)) { + rhist = hist(rawrs[,i],breaks=100,plot=F) + m = append(m,max(rhist\$counts)) + } + ymax = max(m) + ncols = length(fullnames) + if (ncols > 20) + { + scale = 7*ncols/20 + pdf(pdfname,width=scale,height=scale) + } else { + pdf(pdfname) + } + par(mfrow=c(ncroot,ncroot)) + for (i in c(1:nc)) { + hist(rawrs[,i], main=paste("Contig logcount",i), xlab='log raw count', col="maroon", + breaks=100,sub=fullnames[i],cex=0.8,ylim=c(0,ymax)) + } + dev.off() + par(defpar) + +} + +cumPlot = function(rawrs,cleanrs,maint,myTitle) +{ # updated to use ecdf + pdfname = "Filtering_rowsum_bar_charts.pdf" + defpar = par(no.readonly=T) + lrs = log(rawrs,10) + lim = max(lrs) + pdf(pdfname) + par(mfrow=c(2,1)) + hist(lrs,breaks=100,main=paste('Before:',maint),xlab="# Reads (log)", + ylab="Count",col="maroon",sub=myTitle, xlim=c(0,lim),las=1) + grid(col="lightgray", lty="dotted") + lrs = log(cleanrs,10) + hist(lrs,breaks=100,main=paste('After:',maint),xlab="# Reads (log)", + ylab="Count",col="maroon",sub=myTitle,xlim=c(0,lim),las=1) + grid(col="lightgray", lty="dotted") + dev.off() + par(defpar) +} + +cumPlot1 = function(rawrs,cleanrs,maint,myTitle) +{ # updated to use ecdf + pdfname = paste(gsub(" ","", myTitle , fixed=TRUE),"RowsumCum.pdf",sep='_') + pdf(pdfname) + par(mfrow=c(2,1)) + lastx = max(rawrs) + rawe = knots(ecdf(rawrs)) + cleane = knots(ecdf(cleanrs)) + cy = 1:length(cleane)/length(cleane) + ry = 1:length(rawe)/length(rawe) + plot(rawe,ry,type='l',main=paste('Before',maint),xlab="Log Contig Total Reads", + ylab="Cumulative proportion",col="maroon",log='x',xlim=c(1,lastx),sub=myTitle) + grid(col="blue") + plot(cleane,cy,type='l',main=paste('After',maint),xlab="Log Contig Total Reads", + ylab="Cumulative proportion",col="maroon",log='x',xlim=c(1,lastx),sub=myTitle) + grid(col="blue") + dev.off() +} + + + +doGSEA = function(y=NULL,design=NULL,histgmt="", + bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt", + ntest=0, myTitle="myTitle", outfname="GSEA.xls", minnin=5, maxnin=2000,fdrthresh=0.05,fdrtype="BH") +{ + sink('Camera.log') + genesets = c() + if (bigmt > "") + { + bigenesets = readLines(bigmt) + genesets = bigenesets + } + if (histgmt > "") + { + hgenesets = readLines(histgmt) + if (bigmt > "") { + genesets = rbind(genesets,hgenesets) + } else { + genesets = hgenesets + } # use only history if no bi + } + print.noquote(paste("@@@read",length(genesets), 'genesets from',histgmt,bigmt)) + genesets = strsplit(genesets,'\t') # tabular. genesetid\tURLorwhatever\tgene_1\t..\tgene_n + outf = outfname + head=paste(myTitle,'edgeR GSEA') + write(head,file=outfname,append=F) + ntest=length(genesets) + urownames = toupper(rownames(y)) + upcam = c() + downcam = c() + for (i in 1:ntest) { + gs = unlist(genesets[i]) + g = gs[1] # geneset_id + u = gs[2] + if (u > "") { u = paste("<a href=\'",u,"\'>",u,"</a>",sep="") } + glist = gs[3:length(gs)] # member gene symbols + glist = toupper(glist) + inglist = urownames %in% glist + nin = sum(inglist) + if ((nin > minnin) && (nin < maxnin)) { + ### print(paste('@@found',sum(inglist),'genes in glist')) + camres = camera(y=y,index=inglist,design=design) + if (! is.null(camres)) { + rownames(camres) = g # gene set name + camres = cbind(GeneSet=g,URL=u,camres) + if (camres\$Direction == "Up") + { + upcam = rbind(upcam,camres) } else { + downcam = rbind(downcam,camres) + } + } + } + } + uscam = upcam[order(upcam\$PValue),] + unadjp = uscam\$PValue + uscam\$adjPValue = p.adjust(unadjp,method=fdrtype) + nup = max(10,sum((uscam\$adjPValue < fdrthresh))) + dscam = downcam[order(downcam\$PValue),] + unadjp = dscam\$PValue + dscam\$adjPValue = p.adjust(unadjp,method=fdrtype) + ndown = max(10,sum((dscam\$adjPValue < fdrthresh))) + write.table(uscam,file=paste('camera_up',outfname,sep='_'),quote=F,sep='\t',row.names=F) + write.table(dscam,file=paste('camera_down',outfname,sep='_'),quote=F,sep='\t',row.names=F) + print.noquote(paste('@@@@@ Camera up top',nup,'gene sets:')) + write.table(head(uscam,nup),file="",quote=F,sep='\t',row.names=F) + print.noquote(paste('@@@@@ Camera down top',ndown,'gene sets:')) + write.table(head(dscam,ndown),file="",quote=F,sep='\t',row.names=F) + sink() +} + + + + +doGSEAatonce = function(y=NULL,design=NULL,histgmt="", + bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt", + ntest=0, myTitle="myTitle", outfname="GSEA.xls", minnin=5, maxnin=2000,fdrthresh=0.05,fdrtype="BH") +{ + sink('Camera.log') + genesets = c() + if (bigmt > "") + { + bigenesets = readLines(bigmt) + genesets = bigenesets + } + if (histgmt > "") + { + hgenesets = readLines(histgmt) + if (bigmt > "") { + genesets = rbind(genesets,hgenesets) + } else { + genesets = hgenesets + } # use only history if no bi + } + print.noquote(paste("@@@read",length(genesets), 'genesets from',histgmt,bigmt)) + genesets = strsplit(genesets,'\t') # tabular. genesetid\tURLorwhatever\tgene_1\t..\tgene_n + outf = outfname + head=paste(myTitle,'edgeR GSEA') + write(head,file=outfname,append=F) + ntest=length(genesets) + urownames = toupper(rownames(y)) + upcam = c() + downcam = c() + incam = c() + urls = c() + gsids = c() + for (i in 1:ntest) { + gs = unlist(genesets[i]) + gsid = gs[1] # geneset_id + url = gs[2] + if (url > "") { url = paste("<a href=\'",url,"\'>",url,"</a>",sep="") } + glist = gs[3:length(gs)] # member gene symbols + glist = toupper(glist) + inglist = urownames %in% glist + nin = sum(inglist) + if ((nin > minnin) && (nin < maxnin)) { + incam = c(incam,inglist) + gsids = c(gsids,gsid) + urls = c(urls,url) + } + } + incam = as.list(incam) + names(incam) = gsids + allcam = camera(y=y,index=incam,design=design) + allcamres = cbind(geneset=gsids,allcam,URL=urls) + for (i in 1:ntest) { + camres = allcamres[i] + res = try(test = (camres\$Direction == "Up")) + if ("try-error" %in% class(res)) { + cat("test failed, camres = :") + print.noquote(camres) + } else { if (camres\$Direction == "Up") + { upcam = rbind(upcam,camres) + } else { downcam = rbind(downcam,camres) + } + + } + } + uscam = upcam[order(upcam\$PValue),] + unadjp = uscam\$PValue + uscam\$adjPValue = p.adjust(unadjp,method=fdrtype) + nup = max(10,sum((uscam\$adjPValue < fdrthresh))) + dscam = downcam[order(downcam\$PValue),] + unadjp = dscam\$PValue + dscam\$adjPValue = p.adjust(unadjp,method=fdrtype) + ndown = max(10,sum((dscam\$adjPValue < fdrthresh))) + write.table(uscam,file=paste('camera_up',outfname,sep='_'),quote=F,sep='\t',row.names=F) + write.table(dscam,file=paste('camera_down',outfname,sep='_'),quote=F,sep='\t',row.names=F) + print.noquote(paste('@@@@@ Camera up top',nup,'gene sets:')) + write.table(head(uscam,nup),file="",quote=F,sep='\t',row.names=F) + print.noquote(paste('@@@@@ Camera down top',ndown,'gene sets:')) + write.table(head(dscam,ndown),file="",quote=F,sep='\t',row.names=F) + sink() + } + + +edgeIt = function (Count_Matrix=c(),group=c(),out_edgeR=F,out_VOOM=F,out_DESeq2=F,fdrtype='fdr',priordf=5, + fdrthresh=0.05,outputdir='.', myTitle='Differential Counts',libSize=c(),useNDF=F, + filterquantile=0.2, subjects=c(),mydesign=NULL, + doDESeq2=T,doVoom=T,doCamera=T,doedgeR=T,org='hg19', + histgmt="", bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt", + doCook=F,DESeq_fitType="parameteric") +{ + # Error handling + if (length(unique(group))!=2){ + print("Number of conditions identified in experiment does not equal 2") + q() + } + require(edgeR) + options(width = 512) + mt = paste(unlist(strsplit(myTitle,'_')),collapse=" ") + allN = nrow(Count_Matrix) + nscut = round(ncol(Count_Matrix)/2) + colTotmillionreads = colSums(Count_Matrix)/1e6 + counts.dataframe = as.data.frame(c()) + rawrs = rowSums(Count_Matrix) + nonzerod = Count_Matrix[(rawrs > 0),] # remove all zero count genes + nzN = nrow(nonzerod) + nzrs = rowSums(nonzerod) + zN = allN - nzN + print('# Quantiles for non-zero row counts:',quote=F) + print(quantile(nzrs,probs=seq(0,1,0.1)),quote=F) + if (useNDF == T) + { + gt1rpin3 = rowSums(Count_Matrix/expandAsMatrix(colTotmillionreads,dim(Count_Matrix)) >= 1) >= nscut + lo = colSums(Count_Matrix[!gt1rpin3,]) + workCM = Count_Matrix[gt1rpin3,] + cleanrs = rowSums(workCM) + cleanN = length(cleanrs) + meth = paste( "After removing",length(lo),"contigs with fewer than ",nscut," sample read counts >= 1 per million, there are",sep="") + print(paste("Read",allN,"contigs. Removed",zN,"contigs with no reads.",meth,cleanN,"contigs"),quote=F) + maint = paste('Filter >=1/million reads in >=',nscut,'samples') + } else { + useme = (nzrs > quantile(nzrs,filterquantile)) + workCM = nonzerod[useme,] + lo = colSums(nonzerod[!useme,]) + cleanrs = rowSums(workCM) + cleanN = length(cleanrs) + meth = paste("After filtering at count quantile =",filterquantile,", there are",sep="") + print(paste('Read',allN,"contigs. Removed",zN,"with no reads.",meth,cleanN,"contigs"),quote=F) + maint = paste('Filter below',filterquantile,'quantile') + } + cumPlot(rawrs=rawrs,cleanrs=cleanrs,maint=maint,myTitle=myTitle) + allgenes = rownames(workCM) + reg = "^chr([0-9]+):([0-9]+)-([0-9]+)" + genecards="<a href=\'http://www.genecards.org/index.php?path=/Search/keyword/" + ucsc = paste("<a href=\'http://genome.ucsc.edu/cgi-bin/hgTracks?db=",org,sep='') + testreg = str_match(allgenes,reg) + if (sum(!is.na(testreg[,1]))/length(testreg[,1]) > 0.8) # is ucsc style string + { + print("@@ using ucsc substitution for urls") + contigurls = paste0(ucsc,"&position=chr",testreg[,2],":",testreg[,3],"-",testreg[,4],"\'>",allgenes,"</a>") + } else { + print.noquote("@@ using genecards substitution for urls") + contigurls = paste0(genecards,allgenes,"\'>",allgenes,"</a>") + } + print(paste("# Total low count contigs per sample = ",paste(lo,collapse=',')),quote=F) + cmrowsums = rowSums(workCM) + TName=unique(group)[1] + CName=unique(group)[2] + if (is.null(mydesign)) { + if (length(subjects) == 0) + { + mydesign = model.matrix(~group) + } + else { + subjf = factor(subjects) + mydesign = model.matrix(~subjf+group) # we block on subject so make group last to simplify finding it + } + } + print.noquote(paste('Using samples:',paste(colnames(workCM),collapse=','))) + print.noquote('Using design matrix:') + print.noquote(mydesign) + if (doedgeR) { + sink('edgeR.log') + #### Setup DGEList object + DGEList = DGEList(counts=workCM, group = group) + DGEList = calcNormFactors(DGEList) + + DGEList = estimateGLMCommonDisp(DGEList,mydesign) + comdisp = DGEList\$common.dispersion + DGEList = estimateGLMTrendedDisp(DGEList,mydesign) + if (edgeR_priordf > 0) { + print.noquote(paste("prior.df =",edgeR_priordf)) + DGEList = estimateGLMTagwiseDisp(DGEList,mydesign,prior.df = edgeR_priordf) + } else { + DGEList = estimateGLMTagwiseDisp(DGEList,mydesign) + } + DGLM = glmFit(DGEList,design=mydesign) + DE = glmLRT(DGLM,coef=ncol(DGLM\$design)) # always last one - subject is first if needed + efflib = DGEList\$samples\$lib.size*DGEList\$samples\$norm.factors + normData = (1e+06*DGEList\$counts/efflib) + uoutput = cbind( + Name=as.character(rownames(DGEList\$counts)), + DE\$table, + adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype), + Dispersion=DGEList\$tagwise.dispersion,totreads=cmrowsums,normData, + DGEList\$counts + ) + soutput = uoutput[order(DE\$table\$PValue),] # sorted into p value order - for quick toptable + goodness = gof(DGLM, pcutoff=fdrthresh) + if (sum(goodness\$outlier) > 0) { + print.noquote('GLM outliers:') + print(paste(rownames(DGLM)[(goodness\$outlier)],collapse=','),quote=F) + } else { + print('No GLM fit outlier genes found\n') + } + z = limma::zscoreGamma(goodness\$gof.statistic, shape=goodness\$df/2, scale=2) + pdf("edgeR_GoodnessofFit.pdf") + qq = qqnorm(z, panel.first=grid(), main="tagwise dispersion") + abline(0,1,lwd=3) + points(qq\$x[goodness\$outlier],qq\$y[goodness\$outlier], pch=16, col="maroon") + dev.off() + estpriorn = getPriorN(DGEList) + print(paste("Common Dispersion =",comdisp,"CV = ",sqrt(comdisp),"getPriorN = ",estpriorn),quote=F) + efflib = DGEList\$samples\$lib.size*DGEList\$samples\$norm.factors + normData = (1e+06*DGEList\$counts)/efflib + lnormData = log(normData + 1e-6,10) + uniqueg = unique(group) + #### Plot MDS + sample_colors = match(group,levels(group)) + sampleTypes = levels(factor(group)) + print.noquote(sampleTypes) + pdf("edgeR_MDSplot.pdf") + plotMDS.DGEList(DGEList,main=paste("edgeR MDS for",myTitle),cex=0.5,col=sample_colors,pch=sample_colors) + legend(x="topleft", legend = sampleTypes,col=c(1:length(sampleTypes)), pch=19) + grid(col="blue") + dev.off() + colnames(normData) = paste( colnames(normData),'N',sep="_") + print(paste('Raw sample read totals',paste(colSums(nonzerod,na.rm=T),collapse=','))) + nzd = data.frame(log(nonzerod + 1e-2,10)) + try( boxPlot(rawrs=nzd,cleanrs=lnormData,maint='TMM Normalisation',myTitle=myTitle,pdfname="edgeR_raw_norm_counts_box.pdf") ) + write.table(soutput,file=out_edgeR, quote=FALSE, sep="\t",row.names=F) + tt = cbind( + Name=as.character(rownames(DGEList\$counts)), + DE\$table, + adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype), + Dispersion=DGEList\$tagwise.dispersion,totreads=cmrowsums + ) + print.noquote("# edgeR Top tags\n") + tt = cbind(tt,URL=contigurls) # add to end so table isn't laid out strangely + tt = tt[order(DE\$table\$PValue),] + print.noquote(tt[1:50,]) + deTags = rownames(uoutput[uoutput\$adj.p.value < fdrthresh,]) + nsig = length(deTags) + print(paste('#',nsig,'tags significant at adj p=',fdrthresh),quote=F) + deColours = ifelse(deTags,'red','black') + pdf("edgeR_BCV_vs_abundance.pdf") + plotBCV(DGEList, cex=0.3, main="Biological CV vs abundance",col.tagwise=deColours) + dev.off() + dg = DGEList[order(DE\$table\$PValue),] + #normData = (1e+06 * dg\$counts/expandAsMatrix(dg\$samples\$lib.size, dim(dg))) + efflib = dg\$samples\$lib.size*dg\$samples\$norm.factors + normData = (1e+06*dg\$counts/efflib) + outpdfname="edgeR_top_100_heatmap.pdf" + hmap2(normData,nsamp=100,TName=TName,group=group,outpdfname=outpdfname,myTitle=paste('edgeR Heatmap',myTitle)) + outSmear = "edgeR_smearplot.pdf" + outMain = paste("Smear Plot for ",TName,' Vs ',CName,' (FDR@',fdrthresh,' N = ',nsig,')',sep='') + smearPlot(DGEList=DGEList,deTags=deTags, outSmear=outSmear, outMain = outMain) + qqPlot(descr=paste(myTitle,'edgeR adj p QQ plot'),pvector=tt\$adj.p.value,outpdf='edgeR_qqplot.pdf') + norm.factor = DGEList\$samples\$norm.factors + topresults.edgeR = soutput[which(soutput\$adj.p.value < fdrthresh), ] + edgeRcountsindex = which(allgenes %in% rownames(topresults.edgeR)) + edgeRcounts = rep(0, length(allgenes)) + edgeRcounts[edgeRcountsindex] = 1 # Create venn diagram of hits + sink() + } ### doedgeR + if (doDESeq2 == T) + { + sink("DESeq2.log") + # DESeq2 + require('DESeq2') + library('RColorBrewer') + if (length(subjects) == 0) + { + pdata = data.frame(Name=colnames(workCM),Rx=group,row.names=colnames(workCM)) + deSEQds = DESeqDataSetFromMatrix(countData = workCM, colData = pdata, design = formula(~ Rx)) + } else { + pdata = data.frame(Name=colnames(workCM),Rx=group,subjects=subjects,row.names=colnames(workCM)) + deSEQds = DESeqDataSetFromMatrix(countData = workCM, colData = pdata, design = formula(~ subjects + Rx)) + } + #DESeq2 = DESeq(deSEQds,fitType='local',pAdjustMethod=fdrtype) + #rDESeq = results(DESeq2) + #newCountDataSet(workCM, group) + deSeqDatsizefac = estimateSizeFactors(deSEQds) + deSeqDatdisp = estimateDispersions(deSeqDatsizefac,fitType=DESeq_fitType) + resDESeq = nbinomWaldTest(deSeqDatdisp, pAdjustMethod=fdrtype) + rDESeq = as.data.frame(results(resDESeq)) + rDESeq = cbind(Contig=rownames(workCM),rDESeq,NReads=cmrowsums) + srDESeq = rDESeq[order(rDESeq\$pvalue),] + write.table(srDESeq,file=out_DESeq2, quote=FALSE, sep="\t",row.names=F) + qqPlot(descr=paste(myTitle,'DESeq2 adj p qq plot'),pvector=rDESeq\$padj,outpdf='DESeq2_qqplot.pdf') + cat("# DESeq top 50\n") + rDESeq = cbind(Contig=rownames(workCM),rDESeq,NReads=cmrowsums,URL=contigurls) + srDESeq = rDESeq[order(rDESeq\$pvalue),] + print.noquote(srDESeq[1:50,]) + topresults.DESeq = rDESeq[which(rDESeq\$padj < fdrthresh), ] + DESeqcountsindex = which(allgenes %in% rownames(topresults.DESeq)) + DESeqcounts = rep(0, length(allgenes)) + DESeqcounts[DESeqcountsindex] = 1 + pdf("DESeq2_dispersion_estimates.pdf") + plotDispEsts(resDESeq) + dev.off() + ysmall = abs(min(rDESeq\$log2FoldChange)) + ybig = abs(max(rDESeq\$log2FoldChange)) + ylimit = min(4,ysmall,ybig) + pdf("DESeq2_MA_plot.pdf") + plotMA(resDESeq,main=paste(myTitle,"DESeq2 MA plot"),ylim=c(-ylimit,ylimit)) + dev.off() + rlogres = rlogTransformation(resDESeq) + sampledists = dist( t( assay(rlogres) ) ) + sdmat = as.matrix(sampledists) + pdf("DESeq2_sample_distance_plot.pdf") + heatmap.2(sdmat,trace="none",main=paste(myTitle,"DESeq2 sample distances"), + col = colorRampPalette( rev(brewer.pal(9, "RdBu")) )(255)) + dev.off() + ###outpdfname="DESeq2_top50_heatmap.pdf" + ###hmap2(sresDESeq,nsamp=50,TName=TName,group=group,outpdfname=outpdfname,myTitle=paste('DESeq2 vst rlog Heatmap',myTitle)) + sink() + result = try( (ppca = plotPCA( varianceStabilizingTransformation(deSeqDatdisp,blind=T), intgroup=c("Rx","Name")) ) ) + if ("try-error" %in% class(result)) { + print.noquote('DESeq2 plotPCA failed.') + } else { + pdf("DESeq2_PCA_plot.pdf") + #### wtf - print? Seems needed to get this to work + print(ppca) + dev.off() + } + } + + if (doVoom == T) { + sink('Voom.log') + if (doedgeR == F) { + #### Setup DGEList object + DGEList = DGEList(counts=workCM, group = group) + DGEList = calcNormFactors(DGEList) + DGEList = estimateGLMCommonDisp(DGEList,mydesign) + DGEList = estimateGLMTrendedDisp(DGEList,mydesign) + DGEList = estimateGLMTagwiseDisp(DGEList,mydesign) + DGEList = estimateGLMTagwiseDisp(DGEList,mydesign) + norm.factor = DGEList\$samples\$norm.factors + } + pdf("Voom_mean_variance_plot.pdf") + dat.voomed = voom(DGEList, mydesign, plot = TRUE, lib.size = colSums(workCM) * norm.factor) + dev.off() + # Use limma to fit data + fit = lmFit(dat.voomed, mydesign) + fit = eBayes(fit) + rvoom = topTable(fit, coef = length(colnames(mydesign)), adj = fdrtype, n = Inf, sort="none") + qqPlot(descr=paste(myTitle,'Voom-limma adj p QQ plot'),pvector=rvoom\$adj.P.Val,outpdf='Voom_qqplot.pdf') + rownames(rvoom) = rownames(workCM) + rvoom = cbind(rvoom,NReads=cmrowsums) + srvoom = rvoom[order(rvoom\$P.Value),] + write.table(srvoom,file=out_VOOM, quote=FALSE, sep="\t",row.names=F) + rvoom = cbind(rvoom,URL=contigurls) + deTags = rownames(rvoom[rvoom\$adj.p.value < fdrthresh,]) + nsig = length(deTags) + cat("# Voom top 50\n") + print(srvoom[1:50,]) + normData = srvoom\$E + outpdfname="Voom_top_100_heatmap.pdf" + hmap2(normData,nsamp=100,TName=TName,group=group,outpdfname=outpdfname,myTitle=paste('VOOM Heatmap',myTitle)) + outSmear = "Voom_smearplot.pdf" + outMain = paste("Smear Plot for ",TName,' Vs ',CName,' (FDR@',fdrthresh,' N = ',nsig,')',sep='') + smearPlot(DGEList=rvoom,deTags=deTags, outSmear=outSmear, outMain = outMain) + qqPlot(descr=paste(myTitle,'VOOM adj p QQ plot'),pvector=srvoom\$adj.P.Val,outpdf='Voom_qqplot.pdf') + # Use an FDR cutoff to find interesting samples for edgeR, DESeq and voom/limma + topresults.voom = rvoom[which(rvoom\$adj.P.Val < fdrthresh), ] + voomcountsindex = which(allgenes %in% topresults.voom\$ID) + voomcounts = rep(0, length(allgenes)) + voomcounts[voomcountsindex] = 1 + sink() + } + + if (doCamera) { + doGSEA(y=DGEList,design=mydesign,histgmt=histgmt,bigmt=bigmt,ntest=20,myTitle=myTitle, + outfname=paste(mt,"GSEA.xls",sep="_"),fdrthresh=fdrthresh,fdrtype=fdrtype) + } + + if ((doDESeq2==T) || (doVoom==T) || (doedgeR==T)) { + if ((doVoom==T) && (doDESeq2==T) && (doedgeR==T)) { + vennmain = paste(mt,'Voom,edgeR and DESeq2 overlap at FDR=',fdrthresh) + counts.dataframe = data.frame(edgeR = edgeRcounts, DESeq2 = DESeqcounts, + VOOM_limma = voomcounts, row.names = allgenes) + } else if ((doDESeq2==T) && (doedgeR==T)) { + vennmain = paste(mt,'DESeq2 and edgeR overlap at FDR=',fdrthresh) + counts.dataframe = data.frame(edgeR = edgeRcounts, DESeq2 = DESeqcounts, row.names = allgenes) + } else if ((doVoom==T) && (doedgeR==T)) { + vennmain = paste(mt,'Voom and edgeR overlap at FDR=',fdrthresh) + counts.dataframe = data.frame(edgeR = edgeRcounts, VOOM_limma = voomcounts, row.names = allgenes) + } + + if (nrow(counts.dataframe > 1)) { + counts.venn = vennCounts(counts.dataframe) + vennf = "Venn_significant_genes_overlap.pdf" + pdf(vennf) + vennDiagram(counts.venn,main=vennmain,col="maroon") + dev.off() + } + } #### doDESeq2 or doVoom + +} +#### Done + +###sink(stdout(),append=T,type="message") +builtin_gmt = "" +history_gmt = "" +history_gmt_name = "" +out_edgeR = F +out_DESeq2 = F +out_VOOM = "$out_VOOM" +doDESeq2 = $DESeq2.doDESeq2 # make these T or F +doVoom = $doVoom +doCamera = F +doedgeR = $edgeR.doedgeR +edgeR_priordf = 0 + + +#if $doVoom == "T": + out_VOOM = "$out_VOOM" +#end if + +#if $DESeq2.doDESeq2 == "T": + out_DESeq2 = "$out_DESeq2" + DESeq_fitType = "$DESeq2.DESeq_fitType" +#end if + +#if $edgeR.doedgeR == "T": + out_edgeR = "$out_edgeR" + edgeR_priordf = $edgeR.edgeR_priordf +#end if + + +if (sum(c(doedgeR,doVoom,doDESeq2)) == 0) +{ +write("No methods chosen - nothing to do! Please try again after choosing one or more methods", stderr()) +quit(save="no",status=2) +} + +Out_Dir = "$html_file.files_path" +Input = "$input1" +TreatmentName = "$treatment_name" +TreatmentCols = "$Treat_cols" +ControlName = "$control_name" +ControlCols= "$Control_cols" +org = "$input1.dbkey" +if (org == "") { org = "hg19"} +fdrtype = "$fdrtype" +fdrthresh = $fdrthresh +useNDF = $useNDF +fQ = $fQ # non-differential centile cutoff +myTitle = "$title" +sids = strsplit("$subjectids",',') +subjects = unlist(sids) +nsubj = length(subjects) +TCols = as.numeric(strsplit(TreatmentCols,",")[[1]])-1 +CCols = as.numeric(strsplit(ControlCols,",")[[1]])-1 +cat('Got TCols=') +cat(TCols) +cat('; CCols=') +cat(CCols) +cat('\n') +useCols = c(TCols,CCols) +if (file.exists(Out_Dir) == F) dir.create(Out_Dir) +Count_Matrix = read.table(Input,header=T,row.names=1,sep='\t') #Load tab file assume header +snames = colnames(Count_Matrix) +nsamples = length(snames) +if (nsubj > 0 & nsubj != nsamples) { +options("show.error.messages"=T) +mess = paste('Fatal error: Supplied subject id list',paste(subjects,collapse=','), + 'has length',nsubj,'but there are',nsamples,'samples',paste(snames,collapse=',')) +write(mess, stderr()) +quit(save="no",status=4) +} +if (length(subjects) != 0) {subjects = subjects[useCols]} +Count_Matrix = Count_Matrix[,useCols] ### reorder columns +rn = rownames(Count_Matrix) +islib = rn %in% c('librarySize','NotInBedRegions') +LibSizes = Count_Matrix[subset(rn,islib),][1] # take first +Count_Matrix = Count_Matrix[subset(rn,! islib),] +group = c(rep(TreatmentName,length(TCols)), rep(ControlName,length(CCols)) ) #Build a group descriptor +group = factor(group, levels=c(ControlName,TreatmentName)) +colnames(Count_Matrix) = paste(group,colnames(Count_Matrix),sep="_") #Relable columns +results = edgeIt(Count_Matrix=Count_Matrix,group=group, out_edgeR=out_edgeR, out_VOOM=out_VOOM, out_DESeq2=out_DESeq2, + fdrtype='BH',mydesign=NULL,priordf=edgeR_priordf,fdrthresh=fdrthresh,outputdir='.', + myTitle=myTitle,useNDF=F,libSize=c(),filterquantile=fQ,subjects=subjects, + doDESeq2=doDESeq2,doVoom=doVoom,doCamera=doCamera,doedgeR=doedgeR,org=org, + histgmt=history_gmt,bigmt=builtin_gmt,DESeq_fitType=DESeq_fitType) +sessionInfo() +]]> +</configfile> +</configfiles> +<help> + +**What it does** + +Allows short read sequence counts from controlled experiments to be analysed for differentially expressed genes. +Optionally adds a term for subject if not all samples are independent or if some other factor needs to be blocked in the design. + +**Input** + +Requires a count matrix as a tabular file. These are best made using the companion HTSeq_ based counter Galaxy wrapper +and your fave gene model to generate inputs. Each row is a genomic feature (gene or exon eg) and each column the +non-negative integer count of reads from one sample overlapping the feature. +The matrix must have a header row uniquely identifying the source samples, and unique row names in +the first column. Typically the row names are gene symbols or probe ids for downstream use in GSEA and other methods. + +**Specifying comparisons** + +This is basically dumbed down for two factors - case vs control. + +More complex interfaces are possible but painful at present. +Probably need to specify a phenotype file to do this better. +Work in progress. Send code. + +If you have (eg) paired samples and wish to include a term in the GLM to account for some other factor (subject in the case of paired samples), +put a comma separated list of indicators for every sample (whether modelled or not!) indicating (eg) the subject number or +A list of integers, one for each subject or an empty string if samples are all independent. +If not empty, there must be exactly as many integers in the supplied integer list as there are columns (samples) in the count matrix. +Integers for samples that are not in the analysis *must* be present in the string as filler even if not used. + +So if you have 2 pairs out of 6 samples, you need to put in unique integers for the unpaired ones +eg if you had 6 samples with the first two independent but the second and third pairs each being from independent subjects. you might use +8,9,1,1,2,2 +as subject IDs to indicate two paired samples from the same subject in columns 3/4 and 5/6 + +**Methods available** + +You can run 3 popular Bioconductor packages available for count data. + +edgeR - see edgeR_ for details + +VOOM/limma - see limma_VOOM_ for details + +DESeq2 - see DESeq2_ for details + +and optionally camera in edgeR which works better if MSigDB is installed. + +**Outputs** + +Some helpful plots and analysis results. Note that most of these are produced using R code +suggested by the excellent documentation and vignettes for the Bioconductor +packages invoked. The Tool Factory is used to automatically lay these out for you to enjoy. + +**Note on Voom** + +The voom from limma version 3.16.6 help in R includes this from the authors - but you should read the paper to interpret this method. + +This function is intended to process RNA-Seq or ChIP-Seq data prior to linear modelling in limma. + +voom is an acronym for mean-variance modelling at the observational level. +The key concern is to estimate the mean-variance relationship in the data, then use this to compute appropriate weights for each observation. +Count data almost show non-trivial mean-variance relationships. Raw counts show increasing variance with increasing count size, while log-counts typically show a decreasing mean-variance trend. +This function estimates the mean-variance trend for log-counts, then assigns a weight to each observation based on its predicted variance. +The weights are then used in the linear modelling process to adjust for heteroscedasticity. + +In an experiment, a count value is observed for each tag in each sample. A tag-wise mean-variance trend is computed using lowess. +The tag-wise mean is the mean log2 count with an offset of 0.5, across samples for a given tag. +The tag-wise variance is the quarter-root-variance of normalized log2 counts per million values with an offset of 0.5, across samples for a given tag. +Tags with zero counts across all samples are not included in the lowess fit. Optional normalization is performed using normalizeBetweenArrays. +Using fitted values of log2 counts from a linear model fit by lmFit, variances from the mean-variance trend were interpolated for each observation. +This was carried out by approxfun. Inverse variance weights can be used to correct for mean-variance trend in the count data. + + +Author(s) + +Charity Law and Gordon Smyth + +References + +Law, CW (2013). Precision weights for gene expression analysis. PhD Thesis. University of Melbourne, Australia. + +Law, CW, Chen, Y, Shi, W, Smyth, GK (2013). Voom! Precision weights unlock linear model analysis tools for RNA-seq read counts. +Technical Report 1 May 2013, Bioinformatics Division, Walter and Eliza Hall Institute of Medical Reseach, Melbourne, Australia. +http://www.statsci.org/smyth/pubs/VoomPreprint.pdf + +See Also + +A voom case study is given in the edgeR User's Guide. + +vooma is a similar function but for microarrays instead of RNA-seq. + + +***old rant on changes to Bioconductor package variable names between versions*** + +The edgeR authors made a small cosmetic change in the name of one important variable (from p.value to PValue) +breaking this and all other code that assumed the old name for this variable, +between edgeR2.4.4 and 2.4.6 (the version for R 2.14 as at the time of writing). +This means that all code using edgeR is sensitive to the version. I think this was a very unwise thing +to do because it wasted hours of my time to track down and will similarly cost other edgeR users dearly +when their old scripts break. This tool currently now works with 2.4.6. + +**Note on prior.N** + +http://seqanswers.com/forums/showthread.php?t=5591 says: + +*prior.n* + +The value for prior.n determines the amount of smoothing of tagwise dispersions towards the common dispersion. +You can think of it as like a "weight" for the common value. (It is actually the weight for the common likelihood +in the weighted likelihood equation). The larger the value for prior.n, the more smoothing, i.e. the closer your +tagwise dispersion estimates will be to the common dispersion. If you use a prior.n of 1, then that gives the +common likelihood the weight of one observation. + +In answer to your question, it is a good thing to squeeze the tagwise dispersions towards a common value, +or else you will be using very unreliable estimates of the dispersion. I would not recommend using the value that +you obtained from estimateSmoothing()---this is far too small and would result in virtually no moderation +(squeezing) of the tagwise dispersions. How many samples do you have in your experiment? +What is the experimental design? If you have few samples (less than 6) then I would suggest a prior.n of at least 10. +If you have more samples, then the tagwise dispersion estimates will be more reliable, +so you could consider using a smaller prior.n, although I would hesitate to use a prior.n less than 5. + + +From Bioconductor Digest, Vol 118, Issue 5, Gordon writes: + +Dear Dorota, + +The important settings are prior.df and trend. + +prior.n and prior.df are related through prior.df = prior.n * residual.df, +and your experiment has residual.df = 36 - 12 = 24. So the old setting of +prior.n=10 is equivalent for your data to prior.df = 240, a very large +value. Going the other way, the new setting of prior.df=10 is equivalent +to prior.n=10/24. + +To recover old results with the current software you would use + + estimateTagwiseDisp(object, prior.df=240, trend="none") + +To get the new default from old software you would use + + estimateTagwiseDisp(object, prior.n=10/24, trend=TRUE) + +Actually the old trend method is equivalent to trend="loess" in the new +software. You should use plotBCV(object) to see whether a trend is +required. + +Note you could also use + + prior.n = getPriorN(object, prior.df=10) + +to map between prior.df and prior.n. + +---- + +**Attributions** + +edgeR - edgeR_ + +VOOM/limma - limma_VOOM_ + +DESeq2 - DESeq2_ for details + +See above for Bioconductor package documentation for packages exposed in Galaxy by this tool and app store package. + +Galaxy_ (that's what you are using right now!) for gluing everything together + +Otherwise, all code and documentation comprising this tool was written by Ross Lazarus and is +licensed to you under the LGPL_ like other rgenetics artefacts + +.. _LGPL: http://www.gnu.org/copyleft/lesser.html +.. _HTSeq: http://www-huber.embl.de/users/anders/HTSeq/doc/index.html +.. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html +.. _DESeq2: http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html +.. _limma_VOOM: http://www.bioconductor.org/packages/release/bioc/html/limma.html +.. _Galaxy: http://getgalaxy.org +</help> + +</tool> + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/edgeRtest1out.html Mon Dec 23 21:36:34 2013 -0500 @@ -0,0 +1,733 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> + <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + <meta name="generator" content="Galaxy rgToolFactory.py tool output - see http://g2.trac.bx.psu.edu/" /> + <title></title> + <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> + </head> + <body> + <div class="toolFormBody"> + +<div class="infomessage">Galaxy Tool "DifferentialCounts" run at 07/08/2013 15:46:55</div><br/> +<div class="toolFormTitle">DESeq2 images and outputs</div> +(Click on a thumbnail image to download the corresponding original PDF image)<br/> +<div><table class="simple" cellpadding="2" cellspacing="2"> +<tr> +<td><a href="DESeq2_MA_plot.pdf"><img src="DESeq2_MA_plot.png" title="Click to download a PDF of DESeq2_MA_plot.pdf" hspace="5" width="400" + alt="Image called DESeq2_MA_plot.pdf"/></a></td> + +<td><a href="DESeq2_PCA_plot.pdf"><img src="DESeq2_PCA_plot.png" title="Click to download a PDF of DESeq2_PCA_plot.pdf" hspace="5" width="400" + alt="Image called DESeq2_PCA_plot.pdf"/></a></td> + +<td><a href="DESeq2_dispersion_estimates.pdf"><img src="DESeq2_dispersion_estimates.png" title="Click to download a PDF of DESeq2_dispersion_estimates.pdf" hspace="5" width="400" + alt="Image called DESeq2_dispersion_estimates.pdf"/></a></td> +</tr> +<tr> +<td><a href="DESeq2_qqplot.pdf"><img src="DESeq2_qqplot.png" title="Click to download a PDF of DESeq2_qqplot.pdf" hspace="5" width="400" + alt="Image called DESeq2_qqplot.pdf"/></a></td> + +<td><a href="DESeq2_sample_distance_plot.pdf"><img src="DESeq2_sample_distance_plot.png" title="Click to download a PDF of DESeq2_sample_distance_plot.pdf" hspace="5" width="400" + alt="Image called DESeq2_sample_distance_plot.pdf"/></a></td> + +<td> </td> +</tr></table></div> + +<div class="toolFormTitle">DESeq2 log output</div> + +<pre> + +# DESeq top 50 + + Contig baseMean log2FoldChange lfcSE pvalue padj NReads URL + +Mir192 Mir192 271352.97636 6.965264 0.2150593 4.096936e-230 4.576278e-227 2325567 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'>Mir192</a> + +Mir122a Mir122a 10112.31117 10.312083 0.3292695 2.649323e-215 1.479647e-212 90428 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'>Mir122a</a> + +Mir149 Mir149 810.35429 -6.911118 0.2341392 1.735537e-191 6.461982e-189 6164 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir149'>Mir149</a> + +Mir23a Mir23a 1289.18043 -3.104086 0.1191688 1.424246e-149 3.977206e-147 10118 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23a'>Mir23a</a> + +Mir181d Mir181d 275.22797 -3.581172 0.1778187 3.329371e-90 7.437816e-88 2139 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181d'>Mir181d</a> + +Mir204 Mir204 347.57397 -7.284200 0.3771119 3.959336e-83 7.370965e-81 2601 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'>Mir204</a> + +Mir23b Mir23b 2028.55377 -2.065110 0.1085802 1.182361e-80 1.886711e-78 16387 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23b'>Mir23b</a> + +Mir27a Mir27a 2788.72629 -3.016676 0.1688167 2.036708e-71 2.843754e-69 21886 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'>Mir27a</a> + +Mir195 Mir195 519.86200 -3.152795 0.1784796 7.838123e-70 9.727982e-68 3962 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir195'>Mir195</a> + +Mir194-2 Mir194-2 391.65678 5.222911 0.3099275 1.013490e-63 1.132068e-61 3570 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-2'>Mir194-2</a> + +Mir208b Mir208b 1649.77924 -11.396172 0.6771238 1.464479e-63 1.487112e-61 14756 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208b'>Mir208b</a> + +Mir10b Mir10b 27820.40551 -5.071453 0.3044889 2.754493e-62 2.563974e-60 197340 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'>Mir10b</a> + +Mir181c Mir181c 2765.96510 -3.660964 0.2275711 3.141153e-58 2.698975e-56 23605 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181c'>Mir181c</a> + +Mir208a Mir208a 616.76981 -10.356524 0.6559217 3.688385e-56 2.942804e-54 4638 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208a'>Mir208a</a> + +Mir490 Mir490 220.99790 -8.059660 0.5142876 2.369067e-55 1.764165e-53 1741 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'>Mir490</a> + +Mir203 Mir203 772.92882 1.990849 0.1274099 4.877239e-55 3.404923e-53 6739 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir203'>Mir203</a> + +Mir215 Mir215 152.78082 -3.004380 0.1939090 3.822339e-54 2.511502e-52 1182 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir215'>Mir215</a> + +Dnm3os Dnm3os 179.61643 -3.278392 0.2166491 9.922020e-52 6.157165e-50 1401 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Dnm3os'>Dnm3os</a> + +Mir214 Mir214 134.69038 -3.216444 0.2154916 2.230148e-50 1.311093e-48 1048 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir214'>Mir214</a> + +Mir21 Mir21 26121.31011 2.963903 0.2008617 2.817434e-49 1.573537e-47 229120 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir21'>Mir21</a> + +Mir1948 Mir1948 263.89527 7.074045 0.4867225 7.374030e-48 3.922282e-46 2404 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1948'>Mir1948</a> + +Mir27b Mir27b 76478.05753 -1.904653 0.1312889 1.088626e-47 5.527251e-46 625308 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27b'>Mir27b</a> + +Rabggtb Rabggtb 2257.19195 1.988368 0.1401741 1.134862e-45 5.511484e-44 19535 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rabggtb'>Rabggtb</a> + +Mir499 Mir499 712.45950 -10.577061 0.7528467 7.766408e-45 3.614616e-43 6527 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir499'>Mir499</a> + +Mir101b Mir101b 6846.19683 3.791681 0.2809666 1.670548e-41 7.464007e-40 59019 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir101b'>Mir101b</a> + +Mir132 Mir132 106.46062 -2.797928 0.2083376 4.046163e-41 1.738294e-39 857 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir132'>Mir132</a> + +Mir143hg Mir143hg 180217.77425 -2.169143 0.1685614 6.764675e-38 2.798571e-36 1407364 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143hg'>Mir143hg</a> + +Mir143 Mir143 179219.35960 -2.170303 0.1696199 1.746403e-37 6.966899e-36 1399819 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143'>Mir143</a> + +Mir155 Mir155 57.66182 -3.788079 0.3056585 2.845488e-35 1.096004e-33 463 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir155'>Mir155</a> + +Mir322 Mir322 899.53469 -3.126011 0.2622595 9.363374e-33 3.486296e-31 7074 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir322'>Mir322</a> + +Mir378 Mir378 483.21548 -2.994300 0.2577321 3.343457e-31 1.204723e-29 4075 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir378'>Mir378</a> + +Mir24-2 Mir24-2 424.48288 -2.712674 0.2361028 1.491830e-30 5.049617e-29 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir24-2'>Mir24-2</a> + +Mir3074-2 Mir3074-2 424.48288 -2.712674 0.2361028 1.491830e-30 5.049617e-29 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3074-2'>Mir3074-2</a> + +Mir199b Mir199b 47.84725 -5.294373 0.4644474 4.215162e-30 1.384805e-28 370 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199b'>Mir199b</a> + +Mir802 Mir802 166.83414 8.816580 0.7782636 9.478527e-30 3.025004e-28 1514 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir802'>Mir802</a> + +Mir125b-2 Mir125b-2 493.08516 -2.919341 0.2631193 1.324797e-28 4.110551e-27 3837 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-2'>Mir125b-2</a> + +Mir301 Mir301 260.53406 -1.676984 0.1526772 4.570133e-28 1.379686e-26 2119 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir301'>Mir301</a> + +Snord104 Snord104 3851.90119 2.386573 0.2173857 4.847914e-28 1.425032e-26 33458 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord104'>Snord104</a> + +Mir150 Mir150 553.20599 -2.836881 0.2595088 8.127991e-28 2.327940e-26 4229 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir150'>Mir150</a> + +Mir148a Mir148a 118994.46955 2.678852 0.2481801 3.675045e-27 1.026256e-25 1002397 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir148a'>Mir148a</a> + +5430416N02Rik 5430416N02Rik 62.15966 3.089960 0.2941123 8.101331e-26 2.207119e-24 564 <a href='http://www.genecards.org/index.php?path=/Search/keyword/5430416N02Rik'>5430416N02Rik</a> + +Mir193 Mir193 45.70861 4.991530 0.4814098 3.446492e-25 9.166027e-24 421 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir193'>Mir193</a> + +Mir3073 Mir3073 98.93199 8.208709 0.7944742 5.036320e-25 1.308272e-23 904 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3073'>Mir3073</a> + +Mir125b-1 Mir125b-1 79.01988 -3.020660 0.2937360 8.355633e-25 2.121191e-23 609 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-1'>Mir125b-1</a> + +2610203C20Rik 2610203C20Rik 79.17666 -3.023491 0.2948614 1.136165e-24 2.820214e-23 610 <a href='http://www.genecards.org/index.php?path=/Search/keyword/2610203C20Rik'>2610203C20Rik</a> + +Mir181a-1 Mir181a-1 59.53826 -3.151487 0.3211628 9.923707e-23 2.409735e-21 506 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-1'>Mir181a-1</a> + +Mir184 Mir184 32.23796 -4.865023 0.4962776 1.092606e-22 2.596683e-21 247 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir184'>Mir184</a> + +Mir199a-2 Mir199a-2 44.84878 -3.422216 0.3545647 4.826269e-22 1.123113e-20 352 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199a-2'>Mir199a-2</a> + +Snord91a Snord91a 168.95251 2.700421 0.2835464 1.670595e-21 3.808275e-20 1437 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord91a'>Snord91a</a> + +Mir200b Mir200b 87.13638 5.940702 0.6338554 7.094881e-21 1.584996e-19 888 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200b'>Mir200b</a> + + +</pre> + +<div class="toolFormTitle">DifferentialCounts log output</div> + +<pre> + +Loading required package: gtools + +Loading required package: gdata + +gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED. + +gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED. + +Attaching package: ‘gdata’ + +The following object is masked from ‘package:stats’: + + nobs + +The following object is masked from ‘package:utils’: + + object.size + +Loading required package: caTools + +Loading required package: grid + +Loading required package: KernSmooth + +KernSmooth 2.23 loaded + +Copyright M. P. Wand 1997-2009 + +Loading required package: MASS + +Attaching package: ‘gplots’ + +The following object is masked from ‘package:stats’: + + lowess + +Loading required package: methods + +Loading required package: limma + +Loading required package: splines + +Loading required package: DESeq2 + +Loading required package: GenomicRanges + +Loading required package: BiocGenerics + +Loading required package: parallel + +Attaching package: ‘BiocGenerics’ + +The following object is masked from ‘package:parallel’: + + clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB + +The following object is masked from ‘package:gdata’: + + combine + +The following object is masked from ‘package:stats’: + + xtabs + +The following object is masked from ‘package:base’: + + anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist + +Loading required package: IRanges + +Attaching package: ‘IRanges’ + +The following object is masked from ‘package:gplots’: + + space + +The following object is masked from ‘package:caTools’: + + runmean + +The following object is masked from ‘package:gdata’: + + trim + +Loading required package: Biobase + +Welcome to Bioconductor + + Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. + +Loading required package: lattice + +Loading required package: Rcpp + +Loading required package: RcppArmadillo + +Attaching package: ‘DESeq2’ + +The following object is masked from ‘package:limma’: + + plotMA + +gene-wise dispersion estimates + +mean-dispersion relationship + +final dispersion estimates + +you had estimated dispersions, replacing these + +gene-wise dispersion estimates + +mean-dispersion relationship + +final dispersion estimates + +you had estimated dispersions, replacing these + +gene-wise dispersion estimates + +mean-dispersion relationship + +final dispersion estimates + +Warning messages: + +1: In bplt(at[i], wid = width[i], stats = z$stats[, i], out = z$out[z$group == : + + Outlier (-Inf) in boxplot 1 is not drawn + +2: In bplt(at[i], wid = width[i], stats = z$stats[, i], out = z$out[z$group == : + + Outlier (-Inf) in boxplot 3 is not drawn + +3: In bxp(list(stats = c(-0.430723026286372, -0.127900608036896, 0.474159383291067, : + + some notches went outside hinges ('box'): maybe set notch=FALSE + +4: In par(defpar) : calling par(new=TRUE) with no plot + + +</pre> + +<div class="toolFormTitle">VOOM images and outputs</div> +(Click on a thumbnail image to download the corresponding original PDF image)<br/> +<div><table class="simple" cellpadding="2" cellspacing="2"> +<tr> +<td><a href="VOOM_mean_variance_plot.pdf"><img src="VOOM_mean_variance_plot.png" title="Click to download a PDF of VOOM_mean_variance_plot.pdf" hspace="5" width="400" + alt="Image called VOOM_mean_variance_plot.pdf"/></a></td> + +<td><a href="VOOM_qqplot.pdf"><img src="VOOM_qqplot.png" title="Click to download a PDF of VOOM_qqplot.pdf" hspace="5" width="400" + alt="Image called VOOM_qqplot.pdf"/></a></td> +</tr> + +</table></div> + +<div class="toolFormTitle">VOOM log output</div> + +<pre> + +# VOOM top 50 + + ID logFC AveExpr t P.Value adj.P.Val B NReads URL + +Mir192 Mir192 6.948883 14.6763803 42.722954 2.301199e-16 2.625668e-13 27.266471 2325567 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'>Mir192</a> + +Mir208a Mir208a -11.015018 3.9395538 -23.252407 1.118938e-12 6.383542e-10 17.208662 4638 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208a'>Mir208a</a> + +Mir122a Mir122a 10.426125 8.1698641 21.722912 2.859682e-12 1.087633e-09 17.760171 90428 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'>Mir122a</a> + +Mir149 Mir149 -7.030463 6.3160807 -20.883835 4.915491e-12 1.402144e-09 17.277609 6164 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir149'>Mir149</a> + +Mir208b Mir208b -12.433228 4.6076218 -19.592458 1.179199e-11 2.690931e-09 15.683666 14756 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208b'>Mir208b</a> + +Mir10b Mir10b -5.130915 12.2628672 -18.242023 3.124991e-11 4.963978e-09 16.221503 197340 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'>Mir10b</a> + +Mir143hg Mir143hg -2.249221 16.2444825 -18.082481 3.521739e-11 4.963978e-09 16.026695 1407364 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143hg'>Mir143hg</a> + +Mir143 Mir143 -2.251067 16.2358599 -18.081481 3.524391e-11 4.963978e-09 16.026084 1399819 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143'>Mir143</a> + +Mir499 Mir499 -11.567529 3.7874598 -17.942086 3.915496e-11 4.963978e-09 14.821741 6527 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir499'>Mir499</a> + +Mir802 Mir802 9.158434 2.9157675 17.316522 6.338616e-11 7.232360e-09 14.381577 1514 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir802'>Mir802</a> + +Mir3073 Mir3073 8.420542 2.5457189 16.702657 1.033066e-10 1.036045e-08 13.985845 904 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3073'>Mir3073</a> + +Mir148a Mir148a 2.638213 15.4435820 16.548188 1.171186e-10 1.036045e-08 14.814792 1002397 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir148a'>Mir148a</a> + +Mir101b Mir101b 3.765722 10.8508440 16.538566 1.180419e-10 1.036045e-08 14.900027 59019 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir101b'>Mir101b</a> + +Mir490 Mir490 -8.474378 3.7506957 -16.259650 1.484816e-10 1.210125e-08 13.424617 1741 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'>Mir490</a> + +Mir21 Mir21 2.938537 13.1642917 15.375404 3.148335e-10 2.394833e-08 13.867698 229120 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir21'>Mir21</a> + +Mir181c Mir181c -3.742560 9.6295577 -15.242361 3.537063e-10 2.522368e-08 13.810405 23605 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181c'>Mir181c</a> + +Mir204 Mir204 -7.684425 4.7751735 -15.033484 4.254268e-10 2.855364e-08 12.822427 2601 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'>Mir204</a> + +Mir23a Mir23a -3.165768 8.7896592 -14.631179 6.110682e-10 3.873493e-08 13.269174 10118 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23a'>Mir23a</a> + +Mir181d Mir181d -3.636211 6.3713218 -14.317073 8.157508e-10 4.898798e-08 12.956333 2139 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181d'>Mir181d</a> + +Mir133b Mir133b -6.493549 1.2544862 -13.969968 1.129934e-09 6.446275e-08 11.982684 159 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133b'>Mir133b</a> + +Mir27a Mir27a -3.106935 9.9255796 -13.838251 1.281011e-09 6.960160e-08 12.513086 21886 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'>Mir27a</a> + +Mir194-2 Mir194-2 5.264136 6.0897615 13.044012 2.792884e-09 1.448491e-07 11.715753 3570 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-2'>Mir194-2</a> + +Mir195 Mir195 -3.216595 7.4509350 -12.869478 3.332788e-09 1.653353e-07 11.587523 3962 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir195'>Mir195</a> + +Mir27b Mir27b -1.976376 15.0957731 -11.756036 1.082197e-08 5.144946e-07 10.127719 625308 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27b'>Mir27b</a> + +Mir378 Mir378 -3.097393 7.3832049 -11.684163 1.171371e-08 5.346138e-07 10.329692 4075 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir378'>Mir378</a> + +Snord104 Snord104 2.337374 10.6109024 11.495675 1.444482e-08 6.339052e-07 10.023395 33458 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord104'>Snord104</a> + +Mir1983 Mir1983 -5.895500 0.9931851 -11.445812 1.527548e-08 6.441605e-07 9.749260 101 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1983'>Mir1983</a> + +Mir322 Mir322 -3.296618 8.2153415 -11.415362 1.580762e-08 6.441605e-07 10.008472 7074 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir322'>Mir322</a> + +Mir200a Mir200a 6.191561 1.7981309 11.322172 1.756229e-08 6.909853e-07 9.662295 264 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200a'>Mir200a</a> + +Mir215 Mir215 -3.045873 5.7544234 -11.148134 2.141822e-08 8.082459e-07 9.753268 1182 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir215'>Mir215</a> + +Dnm3os Dnm3os -3.363344 5.8607432 -11.092261 2.283960e-08 8.082459e-07 9.689496 1401 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Dnm3os'>Dnm3os</a> + +Mir182 Mir182 4.903995 7.1511683 11.074468 2.331304e-08 8.082459e-07 9.658842 7189 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir182'>Mir182</a> + +Mir181a-2 Mir181a-2 -3.048298 6.9414651 -11.072128 2.337609e-08 8.082459e-07 9.644017 2817 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-2'>Mir181a-2</a> + +Mir1948 Mir1948 7.195525 4.5513493 11.005492 2.524936e-08 8.473388e-07 9.341794 2404 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1948'>Mir1948</a> + +Mir214 Mir214 -3.280874 5.4784451 -10.768257 3.332555e-08 1.086413e-06 9.318504 1048 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir214'>Mir214</a> + +Mir153 Mir153 -5.963803 1.4386315 -10.727082 3.498742e-08 1.093990e-06 9.035569 140 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir153'>Mir153</a> + +Cyp3a25 Cyp3a25 6.318200 1.4888933 10.698226 3.620443e-08 1.093990e-06 9.024973 226 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Cyp3a25'>Cyp3a25</a> + +Gm5441 Gm5441 -5.982176 1.4484953 -10.692891 3.643436e-08 1.093990e-06 9.000362 142 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm5441'>Gm5441</a> + +Mir125b-2 Mir125b-2 -3.077678 7.4316058 -10.446668 4.893073e-08 1.431538e-06 8.884250 3837 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-2'>Mir125b-2</a> + +Mir133a-1 Mir133a-1 -5.144671 0.5903264 -10.358205 5.447229e-08 1.553822e-06 8.575535 60 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133a-1'>Mir133a-1</a> + +1110038B12Rik 1110038B12Rik 2.226702 10.8487089 10.194609 6.655312e-08 1.852125e-06 8.439308 37066 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1110038B12Rik'>1110038B12Rik</a> + +Mir132 Mir132 -2.847559 5.3211839 -10.110952 7.380297e-08 2.004981e-06 8.531491 857 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir132'>Mir132</a> + +Rabggtb Rabggtb 1.935779 9.9874171 9.928995 9.262821e-08 2.457879e-06 8.133384 19535 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rabggtb'>Rabggtb</a> + +Mir504 Mir504 -5.256127 0.6221088 -9.892894 9.693595e-08 2.513725e-06 8.068853 69 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir504'>Mir504</a> + +Mir150 Mir150 -2.938531 7.6297870 -9.842102 1.033602e-07 2.620755e-06 8.116464 4229 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir150'>Mir150</a> + +Mir199b Mir199b -5.752816 2.8805143 -9.823920 1.057683e-07 2.623514e-06 7.979387 370 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199b'>Mir199b</a> + +Mir23b Mir23b -2.124129 9.8141190 -9.806316 1.081569e-07 2.625681e-06 7.979464 16387 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23b'>Mir23b</a> + +Mir24-2 Mir24-2 -2.833979 7.3083691 -9.767192 1.136724e-07 2.646944e-06 8.030550 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir24-2'>Mir24-2</a> + +Mir3074-2 Mir3074-2 -2.833979 7.3083691 -9.767192 1.136724e-07 2.646944e-06 8.030550 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3074-2'>Mir3074-2</a> + +Mir155 Mir155 -3.906600 3.9899000 -9.732173 1.188627e-07 2.712448e-06 8.046518 463 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir155'>Mir155</a> + + +</pre> + +<div class="toolFormTitle">edgeR images and outputs</div> +(Click on a thumbnail image to download the corresponding original PDF image)<br/> +<div><table class="simple" cellpadding="2" cellspacing="2"> +<tr> +<td><a href="edgeR_BCV_vs_abundance.pdf"><img src="edgeR_BCV_vs_abundance.png" title="Click to download a PDF of edgeR_BCV_vs_abundance.pdf" hspace="5" width="400" + alt="Image called edgeR_BCV_vs_abundance.pdf"/></a></td> + +<td><a href="edgeR_GoodnessofFit.pdf"><img src="edgeR_GoodnessofFit.png" title="Click to download a PDF of edgeR_GoodnessofFit.pdf" hspace="5" width="400" + alt="Image called edgeR_GoodnessofFit.pdf"/></a></td> + +<td><a href="edgeR_MDSplot.pdf"><img src="edgeR_MDSplot.png" title="Click to download a PDF of edgeR_MDSplot.pdf" hspace="5" width="400" + alt="Image called edgeR_MDSplot.pdf"/></a></td> +</tr> +<tr> +<td><a href="edgeR_qqplot.pdf"><img src="edgeR_qqplot.png" title="Click to download a PDF of edgeR_qqplot.pdf" hspace="5" width="400" + alt="Image called edgeR_qqplot.pdf"/></a></td> + +<td><a href="edgeR_raw_norm_counts_box.pdf"><img src="edgeR_raw_norm_counts_box.png" title="Click to download a PDF of edgeR_raw_norm_counts_box.pdf" hspace="5" width="400" + alt="Image called edgeR_raw_norm_counts_box.pdf"/></a></td> + +<td><a href="edgeR_smearplot.pdf"><img src="edgeR_smearplot.png" title="Click to download a PDF of edgeR_smearplot.pdf" hspace="5" width="400" + alt="Image called edgeR_smearplot.pdf"/></a></td> +</tr> +<tr> +<td><a href="edgeR_top_100_heatmap.pdf"><img src="edgeR_top_100_heatmap.png" title="Click to download a PDF of edgeR_top_100_heatmap.pdf" hspace="5" width="400" + alt="Image called edgeR_top_100_heatmap.pdf"/></a></td> + +<td> </td><td> </td> +</tr></table></div> + +<div class="toolFormTitle">edgeR log output</div> + +<pre> + +[1] prior.df = 8 + +[1] "No GLM fit outlier genes found\n" + +[1] Common Dispersion = 0.228651460998105 CV = 0.478175136323613 getPriorN = 3.33333333333333 + +[1] heart liver + +[1] "Raw sample read totals 2443751,1644652,1682104,1806045,1440960,1341813,2888924,1428365" + +[1] raw contig counts by sample: + + liver_X11706Liv_CAAA liver_X11700Liv_ATTC liver_X11698Liv_ACTG liver_X11699Liv_ATGA heart_X11706He_AGTTC heart_X11699He_GGCTA heart_X11698He_TAGCT heart_X11700He_CTTGT + + Min. :0.0043 Min. :0.0043 Min. :0.0043 Min. :0.0043 Min. :0.0043 Min. :0.0043 Min. :0.0043 Min. :0.0043 + + 1st Qu.:0.3032 1st Qu.:0.0043 1st Qu.:0.3032 1st Qu.:0.0043 1st Qu.:0.0043 1st Qu.:0.0043 1st Qu.:0.0043 1st Qu.:0.0043 + + Median :0.7789 Median :0.6031 Median :0.6998 Median :0.6031 Median :0.4786 Median :0.4786 Median :0.4786 Median :0.4786 + + Mean :1.0519 Mean :1.0343 Mean :0.9855 Mean :0.9966 Mean :0.9210 Mean :0.9428 Mean :1.0205 Mean :0.9753 + + 3rd Qu.:1.5410 3rd Qu.:1.6335 3rd Qu.:1.4473 3rd Qu.:1.5534 3rd Qu.:1.5770 3rd Qu.:1.5855 3rd Qu.:1.7161 3rd Qu.:1.6022 + + Max. :5.8209 Max. :5.6905 Max. :5.7999 Max. :5.7215 Max. :5.3609 Max. :5.3589 Max. :5.6967 Max. :5.3702 + + NA's :650 NA's :969 NA's :664 NA's :886 NA's :902 NA's :957 NA's :821 NA's :950 + +[1] normalised contig counts by sample: + + liver_X11706Liv_CAAA liver_X11700Liv_ATTC liver_X11698Liv_ACTG liver_X11699Liv_ATGA heart_X11706He_AGTTC heart_X11699He_GGCTA heart_X11698He_TAGCT heart_X11700He_CTTGT + + Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf + + 1st Qu.: 0 1st Qu.:-Inf 1st Qu.: 0 1st Qu.:-Inf 1st Qu.:-Inf 1st Qu.:-Inf 1st Qu.:-Inf 1st Qu.:-Inf + + Median : 0 Median : 0 Median : 0 Median : 0 Median : 0 Median : 0 Median : 0 Median : 0 + + Mean :-Inf Mean :-Inf Mean :-Inf Mean :-Inf Mean :-Inf Mean :-Inf Mean :-Inf Mean :-Inf + + 3rd Qu.: 1 3rd Qu.: 1 3rd Qu.: 1 3rd Qu.: 1 3rd Qu.: 1 3rd Qu.: 1 3rd Qu.: 1 3rd Qu.: 1 + + Max. : 6 Max. : 6 Max. : 6 Max. : 5 Max. : 5 Max. : 5 Max. : 6 Max. : 5 + +[1] Using ncol rawrs= 8 + +[1] # edgeR Top tags\n + + Name logFC logCPM LR PValue adj.p.value Dispersion totreads URL + +Mir208a Mir208a -11.840751 8.465017 594.16946 3.104543e-131 3.542284e-128 0.05171220 4638 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208a'>Mir208a</a> + +Mir149 Mir149 -7.008984 8.861767 484.30321 2.473909e-107 1.411365e-104 0.04959937 6164 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir149'>Mir149</a> + +Mir208b Mir208b -13.291635 9.905945 417.69758 7.737463e-93 2.942815e-90 0.10508096 14756 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208b'>Mir208b</a> + +Mir122a Mir122a 10.514683 12.478088 415.17429 2.740525e-92 7.817349e-90 0.10803882 90428 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'>Mir122a</a> + +Mir204 Mir204 -7.498162 7.634507 341.30678 3.313430e-76 7.561247e-74 0.06907958 2601 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'>Mir204</a> + +Mir499 Mir499 -13.577454 8.700078 325.79199 7.930755e-73 1.508165e-70 0.12042284 6527 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir499'>Mir499</a> + +Mir490 Mir490 -8.534394 6.991023 303.17184 6.710366e-68 1.093790e-65 0.07949711 1741 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'>Mir490</a> + +Mir192 Mir192 6.953853 17.169364 217.22867 3.638307e-49 5.189135e-47 0.12700995 2325567 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'>Mir192</a> + +Mir802 Mir802 11.440805 6.593380 212.88059 3.231644e-48 4.097007e-46 0.12273671 1514 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir802'>Mir802</a> + +Mir1948 Mir1948 7.418142 7.252734 195.66958 1.840248e-44 2.099723e-42 0.12060221 2404 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1948'>Mir1948</a> + +Mir194-2 Mir194-2 5.298950 7.811522 191.85588 1.250960e-43 1.297587e-41 0.08670751 3570 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-2'>Mir194-2</a> + +Mir23a Mir23a -3.153807 9.529402 177.53185 1.676248e-40 1.593833e-38 0.04442763 10118 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23a'>Mir23a</a> + +Mir181c Mir181c -3.767686 10.639598 169.87390 7.883295e-39 6.919107e-37 0.06368883 23605 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181c'>Mir181c</a> + +Mir3073 Mir3073 10.686337 5.859950 164.86740 9.778593e-38 7.969554e-36 0.14069249 904 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3073'>Mir3073</a> + +Mir181d Mir181d -3.643963 7.300371 162.18591 3.767663e-37 2.865936e-35 0.05729574 2139 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181d'>Mir181d</a> + +Mir195 Mir195 -3.203683 8.215089 150.20548 1.563314e-34 1.114838e-32 0.05235020 3962 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir195'>Mir195</a> + +Mir10b Mir10b -5.182616 13.946466 147.24793 6.926819e-34 4.649118e-32 0.12268790 197340 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'>Mir10b</a> + +Mir101b Mir101b 3.759962 11.863187 136.31359 1.703812e-31 1.080028e-29 0.07961343 59019 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir101b'>Mir101b</a> + +Mir378 Mir378 -3.115599 8.119617 126.76408 2.092233e-29 1.256441e-27 0.05942391 4075 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir378'>Mir378</a> + +Mir27a Mir27a -3.064687 10.642480 124.98911 5.117477e-29 2.919520e-27 0.06113852 21886 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'>Mir27a</a> + +Mir182 Mir182 5.057509 8.846381 123.17765 1.275060e-28 6.927826e-27 0.13653707 7189 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir182'>Mir182</a> + +Mir322 Mir322 -3.194159 9.012888 107.34926 3.732413e-25 1.935765e-23 0.07536483 7074 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir322'>Mir322</a> + +Mir199b Mir199b -5.520119 4.792610 102.10724 5.259607e-24 2.609223e-22 0.13417024 370 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199b'>Mir199b</a> + +Mir181a-2 Mir181a-2 -3.000177 7.637692 101.38361 7.578821e-24 3.603098e-22 0.06896654 2817 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-2'>Mir181a-2</a> + +Mir125b-2 Mir125b-2 -2.987759 8.144514 91.72544 9.957640e-22 4.488356e-20 0.07737381 3837 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-2'>Mir125b-2</a> + +Dnm3os Dnm3os -3.331215 6.686950 91.67250 1.022763e-21 4.488356e-20 0.08810497 1401 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Dnm3os'>Dnm3os</a> + +Mir184 Mir184 -5.111350 4.234160 84.35542 4.133639e-20 1.686711e-18 0.13502324 247 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir184'>Mir184</a> + +Mir215 Mir215 -3.058208 6.447966 84.35278 4.139167e-20 1.686711e-18 0.08138517 1182 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir215'>Mir215</a> + +Mir133b Mir133b -8.383611 3.584760 83.96681 5.031517e-20 1.960318e-18 0.17482280 159 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133b'>Mir133b</a> + +Mir150 Mir150 -2.883446 8.307765 83.91918 5.154210e-20 1.960318e-18 0.08008123 4229 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir150'>Mir150</a> + +Mir3074-2 Mir3074-2 -2.778308 7.935651 83.74839 5.619282e-20 2.040616e-18 0.07424646 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3074-2'>Mir3074-2</a> + +Mir24-2 Mir24-2 -2.778307 7.935651 83.71222 5.723024e-20 2.040616e-18 0.07427992 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir24-2'>Mir24-2</a> + +Mir193 Mir193 5.176579 4.801090 83.19222 7.445011e-20 2.574169e-18 0.14794861 421 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir193'>Mir193</a> + +Scarna17 Scarna17 2.182159 9.244479 81.91330 1.421894e-19 4.771710e-18 0.04982909 9224 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Scarna17'>Scarna17</a> + +Mir214 Mir214 -3.271172 6.271755 80.43948 2.997458e-19 9.771712e-18 0.09566584 1048 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir214'>Mir214</a> + +Snord104 Snord104 2.330488 11.053611 79.50529 4.809369e-19 1.524303e-17 0.05915990 33458 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord104'>Snord104</a> + +Mir200a Mir200a 7.201555 4.139422 77.35503 1.428304e-18 4.365755e-17 0.19287764 264 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200a'>Mir200a</a> + +Mir200b Mir200b 6.525423 5.752604 77.31985 1.453976e-18 4.365755e-17 0.26237966 888 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200b'>Mir200b</a> + +Mir21 Mir21 2.923147 13.825255 75.51798 3.620938e-18 1.059357e-16 0.09395834 229120 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir21'>Mir21</a> + +Mir203 Mir203 1.956427 8.767610 75.17870 4.299815e-18 1.226522e-16 0.04381710 6739 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir203'>Mir203</a> + +Mir155 Mir155 -3.886731 5.068563 73.81316 8.587210e-18 2.389758e-16 0.12522673 463 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir155'>Mir155</a> + +Cyp3a25 Cyp3a25 8.681501 3.972085 72.29680 1.851471e-17 5.029829e-16 0.23125383 226 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Cyp3a25'>Cyp3a25</a> + +Rabggtb Rabggtb 1.934093 10.298211 72.02043 2.129809e-17 5.651422e-16 0.04596646 19535 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rabggtb'>Rabggtb</a> + +Mir23b Mir23b -2.100584 10.184110 71.44225 2.854935e-17 7.403367e-16 0.05416378 16387 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23b'>Mir23b</a> + +Snord52 Snord52 2.207491 10.217554 71.27974 3.100027e-17 7.860292e-16 0.05941483 18059 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord52'>Snord52</a> + +Gm5441 Gm5441 -6.881248 3.538457 70.05615 5.764004e-17 1.429724e-15 0.20097284 142 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm5441'>Gm5441</a> + +Mir153 Mir153 -6.857671 3.517446 69.37600 8.137282e-17 1.975455e-15 0.20158808 140 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir153'>Mir153</a> + +Mir132 Mir132 -2.858294 5.938312 64.52507 9.531204e-16 2.265647e-14 0.09274248 857 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir132'>Mir132</a> + +1110038B12Rik 1110038B12Rik 2.195962 11.253090 62.92015 2.152583e-15 5.012443e-14 0.06712174 37066 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1110038B12Rik'>1110038B12Rik</a> + +Snord91a Snord91a 2.654072 6.557504 62.40549 2.795431e-15 6.379174e-14 0.08637410 1437 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord91a'>Snord91a</a> + +[1] # 416 tags significant at adj p= 0.05 + + +</pre> + +<div class="toolFormTitle">Other images and outputs</div> +(Click on a thumbnail image to download the corresponding original PDF image)<br/> +<div><table class="simple" cellpadding="2" cellspacing="2"> +<tr> +<td><a href="Filtering_rowsum_bar_charts.pdf"><img src="Filtering_rowsum_bar_charts.png" title="Click to download a PDF of Filtering_rowsum_bar_charts.pdf" hspace="5" width="400" + alt="Image called Filtering_rowsum_bar_charts.pdf"/></a></td> + +<td><a href="Venn_significant_genes_overlap.pdf"><img src="Venn_significant_genes_overlap.png" title="Click to download a PDF of Venn_significant_genes_overlap.pdf" hspace="5" width="400" + alt="Image called Venn_significant_genes_overlap.pdf"/></a></td> +</tr> +<tr> +<td><a href="sample_counts_histogram.pdf"><img src="sample_counts_histogram.png" title="Click to download a PDF of sample_counts_histogram.pdf" hspace="5" width="400" + alt="Image called sample_counts_histogram.pdf"/></a></td> + +<td> </td> +</tr></table></div> + +<div class="toolFormTitle">Other log output</div> + +<pre> + +## Toolfactory generated command line = Rscript - None None + +Got TCols=1 5 6 7; CCols=2 3 4 8 + +[1] # Quantiles for non-zero row counts: + + 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% + + 1.0 1.0 2.0 3.0 4.0 8.0 13.0 24.0 86.6 753.0 2325567.0 + +[1] Read 3242 contigs. Removed 1494 with no reads. After filtering at count quantile =0.3, there are 1141 contigs + +[1] "@@ using genecards substitution for urls" + +[1] # urls + +[1] <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610005C13Rik'>0610005C13Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610007N19Rik'>0610007N19Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610008F07Rik'>0610008F07Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610009L18Rik'>0610009L18Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610012G03Rik'>0610012G03Rik</a> + +[6] <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610031O16Rik'>0610031O16Rik</a> + +[1] # Total low count contigs per sample = 170,67,203,86,145,111,155,120 + +[1] Using samples: liver_X11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam,liver_X11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam,liver_X11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam,liver_X11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam,heart_X11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam,heart_X11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam,heart_X11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam,heart_X11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam + +[1] Using design matrix: + + (Intercept) groupliver + +1 1 1 + +2 1 1 + +3 1 1 + +4 1 1 + +5 1 0 + +6 1 0 + +7 1 0 + +8 1 0 + +attr(,"assign") + +[1] 0 1 + +attr(,"contrasts") + +attr(,"contrasts")$group + +[1] contr.treatment + +R version 3.0.1 (2013-05-16) + +Platform: x86_64-unknown-linux-gnu (64-bit) + +locale: + + [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C + +attached base packages: + + [1] parallel splines methods grid stats graphics grDevices utils datasets base + +other attached packages: + + [1] RColorBrewer_1.0-5 DESeq2_1.0.18 RcppArmadillo_0.3.900.7 Rcpp_0.10.4 lattice_0.20-15 Biobase_2.20.1 GenomicRanges_1.12.4 IRanges_1.18.2 BiocGenerics_0.6.0 edgeR_3.2.4 limma_3.16.7 gplots_2.11.3 MASS_7.3-28 KernSmooth_2.23-10 caTools_1.14 gdata_2.13.2 gtools_3.0.0 stringr_0.6.2 + +loaded via a namespace (and not attached): + + [1] annotate_1.38.0 AnnotationDbi_1.22.6 bitops_1.0-5 DBI_0.2-7 genefilter_1.42.0 locfit_1.5-9.1 RSQLite_0.11.4 stats4_3.0.1 survival_2.37-4 XML_3.98-1.1 xtable_1.7-1 + + +</pre> + +<div class="toolFormTitle">All output files available for downloading</div> + +<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr> + +<tr><td><a href="DESeq2.log">DESeq2.log</a></td><td>10.0 KB</td></tr> +<tr class="odd_row"><td><a href="DESeq2_MA_plot.pdf">DESeq2_MA_plot.pdf</a></td><td>14.7 KB</td></tr> +<tr><td><a href="DESeq2_PCA_plot.pdf">DESeq2_PCA_plot.pdf</a></td><td>4.9 KB</td></tr> +<tr class="odd_row"><td><a href="DESeq2_dispersion_estimates.pdf">DESeq2_dispersion_estimates.pdf</a></td><td>188.4 KB</td></tr> +<tr><td><a href="DESeq2_qqplot.pdf">DESeq2_qqplot.pdf</a></td><td>14.4 KB</td></tr> +<tr class="odd_row"><td><a href="DESeq2_sample_distance_plot.pdf">DESeq2_sample_distance_plot.pdf</a></td><td>9.5 KB</td></tr> +<tr><td><a href="DifferentialCounts.Rscript">DifferentialCounts.Rscript</a></td><td>27.1 KB</td></tr> +<tr class="odd_row"><td><a href="DifferentialCounts_error.log">DifferentialCounts_error.log</a></td><td>3.1 KB</td></tr> +<tr><td><a href="DifferentialCounts_runner.log">DifferentialCounts_runner.log</a></td><td>3.2 KB</td></tr> +<tr class="odd_row"><td><a href="Filtering_rowsum_bar_charts.pdf">Filtering_rowsum_bar_charts.pdf</a></td><td>6.3 KB</td></tr> +<tr><td><a href="VOOM.log">VOOM.log</a></td><td>10.1 KB</td></tr> +<tr class="odd_row"><td><a href="VOOM_mean_variance_plot.pdf">VOOM_mean_variance_plot.pdf</a></td><td>16.7 KB</td></tr> +<tr><td><a href="VOOM_qqplot.pdf">VOOM_qqplot.pdf</a></td><td>17.6 KB</td></tr> +<tr class="odd_row"><td><a href="Venn_significant_genes_overlap.pdf">Venn_significant_genes_overlap.pdf</a></td><td>9.7 KB</td></tr> +<tr><td><a href="edgeR.log">edgeR.log</a></td><td>13.1 KB</td></tr> +<tr class="odd_row"><td><a href="edgeR_BCV_vs_abundance.pdf">edgeR_BCV_vs_abundance.pdf</a></td><td>17.4 KB</td></tr> +<tr><td><a href="edgeR_GoodnessofFit.pdf">edgeR_GoodnessofFit.pdf</a></td><td>13.1 KB</td></tr> +<tr class="odd_row"><td><a href="edgeR_MDSplot.pdf">edgeR_MDSplot.pdf</a></td><td>4.9 KB</td></tr> +<tr><td><a href="edgeR_qqplot.pdf">edgeR_qqplot.pdf</a></td><td>15.2 KB</td></tr> +<tr class="odd_row"><td><a href="edgeR_raw_norm_counts_box.pdf">edgeR_raw_norm_counts_box.pdf</a></td><td>7.8 KB</td></tr> +<tr><td><a href="edgeR_smearplot.pdf">edgeR_smearplot.pdf</a></td><td>16.6 KB</td></tr> +<tr class="odd_row"><td><a href="edgeR_top_100_heatmap.pdf">edgeR_top_100_heatmap.pdf</a></td><td>11.3 KB</td></tr> +<tr><td><a href="sample_counts_histogram.pdf">sample_counts_histogram.pdf</a></td><td>11.0 KB</td></tr> +</table></div><br/> +</div></body></html> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/edgeRtest1out.xls Mon Dec 23 21:36:34 2013 -0500 @@ -0,0 +1,1142 @@ +ID logFC AveExpr t P.Value adj.P.Val B NReads URL +Mir192 6.94888256843679 14.6763802609023 42.7229535356942 2.30119906424271e-16 2.62566813230094e-13 27.2664713266936 2325567 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'>Mir192</a> +Mir208a -11.0150177152075 3.93955375669227 -23.2524066836307 1.11893807599952e-12 6.38354172357727e-10 17.2086622097974 4638 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208a'>Mir208a</a> +Mir122a 10.4261254701779 8.16986409392255 21.7229119192922 2.85968233611017e-12 1.08763251516723e-09 17.760171141852 90428 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'>Mir122a</a> +Mir149 -7.03046258655617 6.31608073609863 -20.8838348040628 4.91549082404237e-12 1.40214375755809e-09 17.2776088871455 6164 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir149'>Mir149</a> +Mir208b -12.4332279840446 4.60762179736006 -19.5924575126382 1.17919871718875e-11 2.69093147262473e-09 15.6836663826186 14756 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208b'>Mir208b</a> +Mir10b -5.1309149063532 12.2628671946242 -18.2420234752943 3.12499057505143e-11 4.96397841614262e-09 16.2215027882858 197340 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'>Mir10b</a> +Mir143hg -2.24922058313374 16.2444825488726 -18.0824813146443 3.52173903971276e-11 4.96397841614262e-09 16.0266951625541 1407364 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143hg'>Mir143hg</a> +Mir143 -2.25106712131643 16.235859869169 -18.0814805993441 3.524391092512e-11 4.96397841614262e-09 16.0260836456534 1399819 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143'>Mir143</a> +Mir499 -11.5675289490546 3.78745976580796 -17.9420857279689 3.91549568319751e-11 4.96397841614262e-09 14.8217405828874 6527 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir499'>Mir499</a> +Mir802 9.15843445824816 2.91576747878654 17.3165224121399 6.33861560587965e-11 7.23236040630868e-09 14.381577240531 1514 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir802'>Mir802</a> +Mir3073 8.42054159318439 2.54571889776166 16.7026571721381 1.03306635740721e-10 1.03604453339228e-08 13.9858447292853 904 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3073'>Mir3073</a> +Mir148a 2.63821345578617 15.4435819751152 16.5481882215215 1.17118649515038e-10 1.03604453339228e-08 14.8147917664862 1002397 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir148a'>Mir148a</a> +Mir101b 3.76572195114225 10.8508440499081 16.5385659719288 1.1804188373444e-10 1.03604453339228e-08 14.9000274171241 59019 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir101b'>Mir101b</a> +Mir490 -8.47437764634465 3.75069567634692 -16.2596504905533 1.48481644820999e-10 1.21012540529114e-08 13.4246171016517 1741 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'>Mir490</a> +Mir21 2.93853744034991 13.1642916950886 15.3754036511693 3.14833456057776e-10 2.39483315574615e-08 13.8676979022068 229120 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir21'>Mir21</a> +Mir181c -3.74256009957124 9.62955774646065 -15.2423608550805 3.53706264458683e-10 2.52236779842098e-08 13.8104046176901 23605 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181c'>Mir181c</a> +Mir204 -7.68442507149438 4.77517348536933 -15.0334839919296 4.2542677795722e-10 2.85536443323052e-08 12.8224274879526 2601 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'>Mir204</a> +Mir23a -3.16576837850821 8.78965917558611 -14.6311785109623 6.11068192724496e-10 3.87349337721472e-08 13.2691736804205 10118 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23a'>Mir23a</a> +Mir181d -3.63621106402109 6.37132182424908 -14.3170733565449 8.15750840848868e-10 4.89879847057136e-08 12.9563328312209 2139 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181d'>Mir181d</a> +Mir133b -6.49354876170712 1.25448620431148 -13.969968060601 1.12993427319653e-09 6.44627502858619e-08 11.9826837063041 159 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133b'>Mir133b</a> +Mir27a -3.10693537246128 9.92557960348829 -13.8382510839158 1.28101104196848e-09 6.96015999469543e-08 12.5130856443239 21886 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'>Mir27a</a> +Mir194-2 5.26413595786074 6.08976151689046 13.0440120203829 2.79288399641768e-09 1.44849119996026e-07 11.7157527118771 3570 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-2'>Mir194-2</a> +Mir195 -3.21659545049586 7.4509349905835 -12.869478368273 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href='http://www.genecards.org/index.php?path=/Search/keyword/Mir182'>Mir182</a> +Mir181a-2 -3.04829832099813 6.94146510070354 -11.0721276255975 2.33760855164295e-08 8.08245865886245e-07 9.64401697815694 2817 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-2'>Mir181a-2</a> +Mir1948 7.19552540631629 4.5513492833967 11.0054920626234 2.52493600829575e-08 8.47338819254543e-07 9.34179361673467 2404 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1948'>Mir1948</a> +Mir214 -3.28087400431203 5.47844506177362 -10.7682572190636 3.3325545851092e-08 1.0864127947456e-06 9.3185039394887 1048 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir214'>Mir214</a> +Mir153 -5.9638030672045 1.43863148956561 -10.7270821099311 3.49874201497232e-08 1.09398957489501e-06 9.03556928822473 140 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir153'>Mir153</a> +Cyp3a25 6.3181999278218 1.48889330889732 10.698226339624 3.62044305804168e-08 1.09398957489501e-06 9.02497280953977 226 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Cyp3a25'>Cyp3a25</a> +Gm5441 -5.98217559924296 1.44849534030207 -10.6928905219357 3.64343591989574e-08 1.09398957489501e-06 9.00036161342169 142 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm5441'>Gm5441</a> +Mir125b-2 -3.07767777869034 7.43160584496732 -10.4466676018996 4.89307304174606e-08 1.43153752323904e-06 8.88425047860251 3837 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-2'>Mir125b-2</a> +Mir133a-1 -5.1446707114636 0.590326422018506 -10.3582048674166 5.44722862183524e-08 1.5538219643785e-06 8.57553468686339 60 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133a-1'>Mir133a-1</a> +1110038B12Rik 2.2267024913641 10.8487089345135 10.1946092089644 6.6553123680318e-08 1.85212473461568e-06 8.43930767784171 37066 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1110038B12Rik'>1110038B12Rik</a> 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href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199b'>Mir199b</a> +Mir23b -2.12412853458823 9.81411903779331 -9.80631552439508 1.08156895246613e-07 2.62568122290182e-06 7.97946421769546 16387 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23b'>Mir23b</a> +Mir24-2 -2.83397931671342 7.30836912335631 -9.76719188905173 1.13672435494913e-07 2.64694385509584e-06 8.03055035937719 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir24-2'>Mir24-2</a> +Mir3074-2 -2.83397931671342 7.30836912335631 -9.76719188905173 1.13672435494913e-07 2.64694385509584e-06 8.03055035937719 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3074-2'>Mir3074-2</a> +Mir155 -3.90660012470502 3.98990000150695 -9.73217278591154 1.18862734970705e-07 2.71244761203149e-06 8.04651834419983 463 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir155'>Mir155</a> +Snord52 2.24297808473649 9.80695706696893 9.65508926768283 1.31194241930095e-07 2.93514960867135e-06 7.78317356265822 18059 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord52'>Snord52</a> +Scarna17 2.22135685073443 8.84690751573681 9.60031550237377 1.4077767610154e-07 3.08898708522803e-06 7.75116302071276 9224 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Scarna17'>Scarna17</a> +Mir201 -5.13478218238105 0.574435171385817 -9.36375298852343 1.91556946938131e-07 4.12389578219637e-06 7.45101629313275 63 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir201'>Mir201</a> +Mir184 -5.19740389169544 2.57741455998865 -9.28503096123923 2.12504578894189e-07 4.42570763295992e-06 7.34294491810118 247 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir184'>Mir184</a> +Snord91a 2.64601724328653 5.9737770599439 9.28208610647144 2.1333384733812e-07 4.42570763295992e-06 7.45176303063652 1437 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord91a'>Snord91a</a> +Mir193 4.93970055277848 3.14663535122407 9.21323530535893 2.33732739541295e-07 4.76230456815389e-06 7.28752724029761 421 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir193'>Mir193</a> +Mir470 5.07947201153691 1.71052510073336 8.84181308472679 3.85901653714362e-07 7.72480327873838e-06 6.83971839651152 157 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir470'>Mir470</a> +0610031O16Rik 4.84298796174609 0.739739561937192 8.8004727262221 4.08431072700958e-07 8.03482506813436e-06 6.77016207746292 78 <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610031O16Rik'>0610031O16Rik</a> +Mir203 1.9396775595845 8.44497102033975 8.70156015908293 4.6818189744087e-07 9.05416177932259e-06 6.53224466632053 6739 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir203'>Mir203</a> +1810019D21Rik 5.37088028736873 1.02158093294187 8.63951664435106 5.10331246821015e-07 9.70479921037964e-06 6.58253399607689 117 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1810019D21Rik'>1810019D21Rik</a> +D7Ertd143e 4.74135480360802 0.690096187370941 8.59182875086527 5.45451616539556e-07 1.02026277782235e-05 6.49996146777963 73 <a href='http://www.genecards.org/index.php?path=/Search/keyword/D7Ertd143e'>D7Ertd143e</a> +Mir181a-1 -3.20886334319296 4.33388500974742 -8.528721562826 5.95908204570219e-07 1.09666332486229e-05 6.48742379588458 506 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-1'>Mir181a-1</a> +Mir547 -4.64199116509563 0.384583900671288 -8.48569977551612 6.33121735643368e-07 1.14665381010966e-05 6.34288346197563 42 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir547'>Mir547</a> +Mir3102 -4.82802034015575 1.26816340424779 -8.40617041640129 7.08539703084848e-07 1.26319343940595e-05 6.2533959548051 87 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3102'>Mir3102</a> +Mir194-1 3.86792676846218 4.28030595336869 8.2361953191898 9.03449017918911e-07 1.5859005068392e-05 6.08687440143381 635 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-1'>Mir194-1</a> +Mir199a-2 -3.62193724804755 3.76746624824118 -8.22528846947687 9.17754251311817e-07 1.58660242537391e-05 6.07294487982063 352 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199a-2'>Mir199a-2</a> +Mir375 4.36561952992499 1.70304479419652 8.20239976081094 9.48559026077637e-07 1.61538186381281e-05 5.9804850351652 123 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir375'>Mir375</a> +Mir128-1 -2.79500838795041 4.68404652058909 -8.16636754121193 9.99287948408945e-07 1.67674639578619e-05 5.95537435854342 527 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir128-1'>Mir128-1</a> +Mir1a-1 -4.50930254765404 0.235845136893643 -8.15352480043541 1.01805558742015e-06 1.68348032644405e-05 5.89233114702952 42 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1a-1'>Mir1a-1</a> +Mir17hg 1.26324530315481 13.08692945461 8.08792426896809 1.11990826888155e-06 1.80004069127122e-05 5.39248242771111 145451 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir17hg'>Mir17hg</a> +Mir92-1 1.26323093975761 13.0869221993444 8.08780961117952 1.12009543453336e-06 1.80004069127122e-05 5.39230857078851 145450 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir92-1'>Mir92-1</a> +Mir881 4.55329779507755 0.622217688176746 7.98090604480001 1.30985575977083e-06 2.06385233899717e-05 5.68307629847666 64 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir881'>Mir881</a> +Mir125b-1 -3.19780406116102 4.7293501044755 -7.96524973476641 1.340381181277e-06 2.06385233899717e-05 5.66721192306587 609 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-1'>Mir125b-1</a> +2610203C20Rik -3.20042083590071 4.73071629949528 -7.96367997663051 1.3434829565975e-06 2.06385233899717e-05 5.66487879544241 610 <a href='http://www.genecards.org/index.php?path=/Search/keyword/2610203C20Rik'>2610203C20Rik</a> +Scnn1b -4.63822537309801 0.37290502628334 -7.9570799219013 1.35660758479218e-06 2.06385233899717e-05 5.63911983957 45 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Scnn1b'>Scnn1b</a> +Mir193b -3.19095319216208 3.51292960275358 -7.90681185253976 1.46112366345347e-06 2.19360802631633e-05 5.62073482323402 260 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir193b'>Mir193b</a> +Mir183 4.30421971951602 3.92737361468754 7.78136892736858 1.76081314682182e-06 2.60215226213659e-05 5.44000583749589 563 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir183'>Mir183</a> +5430416N02Rik 3.07746071410873 4.3937689770433 7.77455061595853 1.77885956570249e-06 2.60215226213659e-05 5.40856341816749 564 <a href='http://www.genecards.org/index.php?path=/Search/keyword/5430416N02Rik'>5430416N02Rik</a> +Mir125a -2.6112312467571 10.9299667279975 -7.67497504879118 2.06586606398761e-06 2.98373820127831e-05 4.87458713303236 37867 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125a'>Mir125a</a> +Mir200b 6.64163006978911 3.12821174098826 7.58298811849222 2.37461716273863e-06 3.38679772835598e-05 5.13195387121669 888 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200b'>Mir200b</a> +C430049B03Rik -1.92074554462898 10.5496297843175 -7.55549117760725 2.4760890707944e-06 3.48792299972396e-05 4.70418935748661 25716 <a href='http://www.genecards.org/index.php?path=/Search/keyword/C430049B03Rik'>C430049B03Rik</a> +Terc 4.24682289892723 0.87844372666952 7.3826580782883 3.2281439398588e-06 4.49184418948646e-05 4.83681905205792 66 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Terc'>Terc</a> +Mir871 5.21513327520529 2.43957936484213 7.24439581531717 4.00226877508459e-06 5.50191406309821e-05 4.63418699567578 290 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir871'>Mir871</a> +Mir30e -1.90475431278526 13.2693114305891 -7.14894534136424 4.6492913699815e-06 6.28199839913465e-05 3.89856793405104 186796 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir30e'>Mir30e</a> +Mir24-1 -3.10183666628555 3.10602318965769 -7.13671325687185 4.73984945200915e-06 6.28199839913465e-05 4.48008371426601 189 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir24-1'>Mir24-1</a> +Mir3074-1 -3.10183666628555 3.10602318965769 -7.13671325687185 4.73984945200915e-06 6.28199839913465e-05 4.48008371426601 189 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3074-1'>Mir3074-1</a> +Mir592 4.27837071128313 0.882966518707851 7.13005059451541 4.78995495814825e-06 6.28199839913465e-05 4.46386515426502 70 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir592'>Mir592</a> +Serpina4-ps1 6.28609584979245 1.44994282762173 7.10887070838901 4.95297318411398e-06 6.42198000349325e-05 4.43976042902202 295 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Serpina4-ps1'>Serpina4-ps1</a> +Mirlet7e -1.98704484524714 6.38418687649397 -6.91936550313624 6.69984149789542e-06 8.58934735853783e-05 3.9044291222869 1576 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mirlet7e'>Mirlet7e</a> +Mir3470b 4.76222273641772 1.545054677666 6.90067154705821 6.90430035193184e-06 8.75311855728247e-05 4.11927719036494 132 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3470b'>Mir3470b</a> +Mir497 -2.37449282835512 5.72555109896591 -6.88407718002354 7.09129622786183e-06 8.89139450108829e-05 3.89837376299718 963 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir497'>Mir497</a> +Mir30d -1.6250750764544 13.1824457426439 -6.86162843142705 7.35278174335401e-06 9.11904779257275e-05 3.42562585807056 161730 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir30d'>Mir30d</a> +Mir107 1.66807649183652 7.69910580818381 6.8393447582273 7.62239107335082e-06 9.35177227386374e-05 3.6976878474277 3843 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir107'>Mir107</a> +Mir301 -1.74763355751926 6.9632575863254 -6.82958967456103 7.7436706688371e-06 9.39949812036503e-05 3.72033936484245 2119 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir301'>Mir301</a> +Mir455 2.46320289727146 5.30404932290074 6.81532109954182 7.92473126605604e-06 9.51801934165257e-05 3.83331724079003 895 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir455'>Mir455</a> +Mir429 4.86439995826456 3.23263249974835 6.78791698606005 8.28507245768243e-06 9.84715382730797e-05 3.94480735955982 499 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir429'>Mir429</a> +1700003L19Rik 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href='http://www.genecards.org/index.php?path=/Search/keyword/Mir31'>Mir31</a> +Mir181b-1 -3.60801009779468 -0.132126628141882 -6.46494720684188 1.41005553764556e-05 0.000157732683181724 3.42410398459059 19 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181b-1'>Mir181b-1</a> +Gm6307 -4.1578316997704 0.656018151435715 -6.45273564502753 1.43909587108892e-05 0.000159418290185675 3.41462429299529 52 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm6307'>Gm6307</a> +Scarna6 1.69929242985022 7.02301841351445 6.42269285853436 1.51324405034754e-05 0.000166020332831399 3.03238527080513 2398 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Scarna6'>Scarna6</a> +Snord45b 1.94022355970573 6.80826479898751 6.39728013438808 1.57909283820436e-05 0.000171594755084873 3.00447879542696 2199 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord45b'>Snord45b</a> +Mir212 -2.84645310030162 3.44913875490104 -6.35557690856707 1.6937466935156e-05 0.000182317450688802 3.21240862806012 232 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir212'>Mir212</a> +Mir488 -4.10203604485773 1.24180834532503 -6.29103817686794 1.88870111723183e-05 0.000201402614463693 3.15543310741006 78 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir488'>Mir488</a> +Mir1943 -2.71589064856915 3.44876720857909 -6.23580114025192 2.07423167962376e-05 0.000219138735782473 3.00834314558259 215 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1943'>Mir1943</a> +Gas5 1.24087717560169 10.5129034284973 6.13133629490868 2.4792457454819e-05 0.000259524715192188 2.31915097100889 24887 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gas5'>Gas5</a> +Mir1960 -3.55886465849503 0.603332307653829 -6.02805967736536 2.96173517543744e-05 0.000307212712288556 2.72737825973636 36 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1960'>Mir1960</a> +Snord72 1.83422077226714 4.99202771858388 6.01300538064759 3.03988327484681e-05 0.000312478091585605 2.48059356064701 603 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord72'>Snord72</a> +Mir126 -1.4123938474776 14.7113257499272 -5.9690966101592 3.28038341776394e-05 0.000334189060684701 1.77670178050375 420720 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir126'>Mir126</a> +Mir181b-2 -3.5537298874584 2.37784481058975 -5.74465057345259 4.86143755138839e-05 0.000490876127976474 2.24688113349229 154 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181b-2'>Mir181b-2</a> +4930581F22Rik 3.25147651228939 0.329341147921603 5.72231806379132 5.05741508633493e-05 0.000506185141535803 2.2176701707354 33 <a href='http://www.genecards.org/index.php?path=/Search/keyword/4930581F22Rik'>4930581F22Rik</a> +Taf1d 1.56967838004803 6.27598295057893 5.62971411199061 5.96235762303463e-05 0.000591569569381088 1.67884064404776 1421 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Taf1d'>Taf1d</a> +Mir324 -2.38077905852261 3.65370681185719 -5.61738196066422 6.09504435595697e-05 0.000599521173288526 1.9104544791018 248 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir324'>Mir324</a> +Mtmr2 -2.30493988089979 4.77764446891153 -5.57410629776523 6.58554908247018e-05 0.000642231752401579 1.7123130370103 580 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mtmr2'>Mtmr2</a> +Mir137 3.41092416262533 0.0324356592441258 5.50287186084007 7.48455682327983e-05 0.000723718587742567 1.84456682895684 29 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir137'>Mir137</a> +Snhg1 0.975366701589908 11.1969347059892 5.49575538415102 7.5811401213261e-05 0.000726897552809502 1.12394645028672 37837 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snhg1'>Snhg1</a> +Mir34a -2.05826883405221 3.36051649740781 -5.47484354411999 7.87253643157781e-05 0.000748547005702523 1.67723038143596 180 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir34a'>Mir34a</a> +Mir298 -3.44904214184284 0.481437816526014 -5.39740371005322 9.05725273791661e-05 0.000854076477187012 1.66441956376117 37 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir298'>Mir298</a> +Mir30b -1.37954359870678 9.2115221848988 -5.37206514503938 9.4840390621554e-05 0.000886990866386828 1.00959570224732 10011 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir30b'>Mir30b</a> +2310001H17Rik 3.60260656982356 0.877139295086231 5.35615735698035 9.76262576906534e-05 0.000902593356272145 1.57720822721783 54 <a href='http://www.genecards.org/index.php?path=/Search/keyword/2310001H17Rik'>2310001H17Rik</a> +Pex16 3.10814004056272 0.242483417469106 5.35355087544425 9.80907766676126e-05 0.000902593356272145 1.58678494520955 30 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Pex16'>Pex16</a> +Mir741 3.33919133389387 0.432231427661093 5.2950378042311 0.000109146860855228 0.000996292545886519 1.47796989545021 36 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir741'>Mir741</a> +Gm6313 -3.15860344908017 -0.430119305523511 -5.24231069726794 0.000120220067795944 0.00108865950281883 1.40353714409938 15 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm6313'>Gm6313</a> +Mir328 -1.36488724959 7.2282210636054 -5.23221518519415 0.000122470141866871 0.00110030261315039 0.870852174596449 2362 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir328'>Mir328</a> +Snord33 1.25647224562943 7.71222650703403 5.19862342341357 0.000130277220055511 0.00116129928190108 0.778490918357933 3442 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord33'>Snord33</a> +Rpph1 1.87063945690961 4.43992987975591 5.19124070458341 0.000132061294296316 0.0011680770293961 1.05386997375291 430 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rpph1'>Rpph1</a> +Mir291a 3.17904342101315 -0.0791999402663102 5.18540568400292 0.000133489301957871 0.00117026083393732 1.2956738181937 24 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir291a'>Mir291a</a> +Mir186 -1.38629871411117 10.176089899221 -5.181881716386 0.000134359482248719 0.00117026083393732 0.594672202880173 18235 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir186'>Mir186</a> +Gm16596 -3.02811906442667 -0.421976649282355 -5.15901843295933 0.000140150118907224 0.00121144913388744 1.25840752971795 12 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm16596'>Gm16596</a> +Mirlet7i -1.21381140575271 10.6031742297066 -5.15326347701587 0.000141648110216644 0.00121519168238489 0.514620675402163 26242 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mirlet7i'>Mirlet7i</a> +Sra1 2.97648314190951 -0.188256184051246 5.14486604509538 0.000143863812461334 0.00122498962700285 1.22868620554498 19 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Sra1'>Sra1</a> +Mir700 -3.05275751205424 3.03686027981893 -5.10658051111472 0.00015443097639702 0.00130522773384445 1.06937466394294 177 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir700'>Mir700</a> +Mir30c-1 -1.44640830149114 5.51774362365196 -5.09058727395353 0.000159080836478697 0.0013266290585589 0.730639691134108 732 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir30c-1'>Mir30c-1</a> +Mir674 -1.94702895981213 4.45877434664642 -5.08988436247691 0.000159288502210841 0.0013266290585589 0.846234772297753 392 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir674'>Mir674</a> +Snord45c 1.44139263505882 6.31780757188042 5.0752407566119 0.000163679307853258 0.00135146340163194 0.643628779392595 1427 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord45c'>Snord45c</a> +Ank1 -1.70157147221109 10.9929711198162 -5.07209350467361 0.000164639275045433 0.00135146340163194 0.337810380148678 33776 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Ank1'>Ank1</a> +Mirlet7b -1.09478453248563 9.30463614623057 -5.06223764308063 0.000167683437276746 0.00136662001380548 0.418305977430397 10012 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mirlet7b'>Mirlet7b</a> +0610008F07Rik 3.20935973501609 0.342617899865038 5.04843460516125 0.000172045196108449 0.00139222389191305 1.0441746904328 34 <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610008F07Rik'>0610008F07Rik</a> +Snord4a 1.57395983217788 5.94089477513251 5.00029990452424 0.000188198499627571 0.00151221470475393 0.535941755206456 1151 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord4a'>Snord4a</a> +Mir3107 -1.70018651164628 9.99212523723331 -4.97672369154541 0.000196676176463643 0.00155838553711817 0.215189363582583 16873 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3107'>Mir3107</a> +Mir486 -1.70018651164628 9.99212523723331 -4.97672369154541 0.000196676176463643 0.00155838553711817 0.215189363582583 16873 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir486'>Mir486</a> +Mir100 -1.97076444192024 8.99815411447499 -4.96949043197095 0.000199355724522589 0.00156872332193292 0.262493038912075 8837 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir100'>Mir100</a> +6430411K18Rik -3.18910263916585 -0.373872894349982 -4.91488268129579 0.000220845557812913 0.00170486995980212 0.826251830470595 17 <a href='http://www.genecards.org/index.php?path=/Search/keyword/6430411K18Rik'>6430411K18Rik</a> +Mir433 -3.18910263916585 -0.373872894349982 -4.91488268129579 0.000220845557812913 0.00170486995980212 0.826251830470595 17 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir433'>Mir433</a> +Mir190 -2.07544392773473 3.1544454577673 -4.91417324518583 0.000221140012314386 0.00170486995980212 0.671557118650327 163 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir190'>Mir190</a> +Mir668 -2.84374273013661 -0.157703843092941 -4.86996462339487 0.000240314465841743 0.00184026043976798 0.746753746471687 15 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir668'>Mir668</a> +0610012G03Rik 2.84115361016785 -0.244188556172649 4.84933497977366 0.000249843031682205 0.00190047266099598 0.705829411755822 17 <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610012G03Rik'>0610012G03Rik</a> +Mirlet7d -1.19906882560952 10.0080528514984 -4.83828196963314 0.000255108219097298 0.00192767203966899 -0.0535917366982233 16847 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mirlet7d'>Mirlet7d</a> +Mir320 -1.40563797109219 6.563348272824 -4.77568906174122 0.000287168062262582 0.00215564973053688 0.0467165593444996 1651 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir320'>Mir320</a> +Snord66 1.15430111322029 8.03351541888005 4.75658981303321 0.00029775850741536 0.00222053893438514 -0.0877963597335594 4212 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord66'>Snord66</a> +Hgd 4.54425664237216 0.975547692617975 4.73952572490202 0.000307561641064749 0.00225560361403978 0.450492806487889 137 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Hgd'>Hgd</a> +Aqp9 4.93135714830861 0.753510541775538 4.73814880056307 0.000308367063909922 0.00225560361403978 0.445426512401092 161 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Aqp9'>Aqp9</a> +Mir221 -1.08377350661343 8.47402248983799 -4.73470478811828 0.000310391167513083 0.00225560361403978 -0.161171563827692 5659 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir221'>Mir221</a> +Atf5 3.74327970750113 0.168725495917353 4.73192727585554 0.00031203354916423 0.00225560361403978 0.467422722695712 50 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Atf5'>Atf5</a> +Ahsg 7.43012370228481 2.43819500653074 4.73140267365542 0.000312344759875797 0.00225560361403978 0.392509485594371 1524 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Ahsg'>Ahsg</a> +Cyp2d13 3.62058562658928 0.099076105394318 4.71784217799444 0.000320501474638856 0.00229995083372915 0.445950346991055 44 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Cyp2d13'>Cyp2d13</a> +Mir292 3.55331832828793 0.0808135496327816 4.67052458846538 0.000350727059524427 0.00250112234323357 0.360392052911509 41 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir292'>Mir292</a> +Proc 4.16579682989808 0.376893953921531 4.63475223165321 0.000375520073648099 0.00266129443498435 0.275862327084029 83 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Proc'>Proc</a> +2610019E17Rik 1.58277820027238 5.58959301890268 4.63093795449771 0.00037826821496869 0.00266422242764985 -0.140287526130874 892 <a href='http://www.genecards.org/index.php?path=/Search/keyword/2610019E17Rik'>2610019E17Rik</a> +Mir379 -2.08294744907303 3.05372097245691 -4.61798165733268 0.000387758909131681 0.00271431236392177 0.128998572399559 153 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir379'>Mir379</a> +Mir96 3.092187161072 -0.127577830654966 4.61264491367143 0.000391739223724717 0.00272545398945063 0.269031262574771 24 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir96'>Mir96</a> +5033403H07Rik 3.03100334960097 -0.167104636116587 4.55138913141517 0.00044055961680218 0.00304390944849929 0.159657330767462 23 <a href='http://www.genecards.org/index.php?path=/Search/keyword/5033403H07Rik'>5033403H07Rik</a> +Mir582 -4.60557103590561 3.35812677089552 -4.5486926708253 0.00044284747454065 0.00304390944849929 0.0591283272554897 566 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir582'>Mir582</a> +Mir335 -1.27174458468766 6.43063411797007 -4.54414079104836 0.000446737391037914 0.00305225965972611 -0.393123932477534 1318 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir335'>Mir335</a> +Gm5424 4.79310957596335 1.09020146508355 4.53505892344961 0.000454603987554657 0.00308751874880871 0.0640172708933422 181 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm5424'>Gm5424</a> +Snord96a 1.64486304749729 4.67116544357615 4.51910388563813 0.0004687711663005 0.00316489882099923 -0.255892987917286 487 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord96a'>Snord96a</a> +Fam120b 3.09294836244015 0.400892342309139 4.51279274228026 0.000474499826623265 0.00318473118927733 0.0711882890790463 39 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Fam120b'>Fam120b</a> +1810032O08Rik 1.41990709594509 5.47749401704587 4.44622801412284 0.000539494231805467 0.00359978314906455 -0.491596569959665 801 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1810032O08Rik'>1810032O08Rik</a> +D830005E20Rik -2.66421484690988 -0.635454055345691 -4.43818702356919 0.00054794279494766 0.00363489958741442 -0.0273233727843643 9 <a href='http://www.genecards.org/index.php?path=/Search/keyword/D830005E20Rik'>D830005E20Rik</a> +Mir3057 -1.76308589999293 3.90842103747244 -4.39033832828025 0.000601107772422842 0.00396453160886973 -0.421971049333088 244 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3057'>Mir3057</a> +Dcaf11 3.64616824902598 1.34504089418874 4.36305371925593 0.000633768357283662 0.00415591779115321 -0.228339632338981 105 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Dcaf11'>Dcaf11</a> +Mir141 2.71262314324362 4.77357067250837 4.34309768158673 0.000658805704226011 0.00429541319155359 -0.576407055554532 835 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir141'>Mir141</a> +Clip4 -2.70686636040313 -0.590132795422603 -4.22339289420565 0.000831845216151027 0.00538076227850526 -0.424317219340228 10 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Clip4'>Clip4</a> +Atp2a2 -3.03468731889576 3.9897529348455 -4.22163834350324 0.000834701948549895 0.00538076227850526 -0.712425757555907 394 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Atp2a2'>Atp2a2</a> +Snord11 1.70196648813426 4.30076703857411 4.20393833047899 0.000864088763598198 0.00553890606328957 -0.81986210274439 399 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord11'>Snord11</a> +Mir1a-2 -2.99188005456984 -0.157703843092941 -4.1964183364679 0.00087689254654494 0.0055585244200432 -0.484125725482271 23 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1a-2'>Mir1a-2</a> +Mir1b -2.99188005456984 -0.157703843092941 -4.1964183364679 0.00087689254654494 0.0055585244200432 -0.484125725482271 23 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1b'>Mir1b</a> +Snord95 0.986915429703335 7.67764085008967 4.16122119437911 0.000939451338082392 0.00592217666713818 -1.23233286437982 3258 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord95'>Snord95</a> +Tardbp 2.97062100907675 0.883541928525332 4.15354257136734 0.000953695266999763 0.00597893571234467 -0.601444869463529 52 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Tardbp'>Tardbp</a> +Mir34c -4.34256582352703 3.19074386781529 -4.14603488500754 0.000967835650645262 0.00601077590779499 -0.705590893704782 715 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir34c'>Mir34c</a> +Nagpa 2.44212396887249 0.350172381597785 4.14525853315587 0.000969310049986221 0.00601077590779499 -0.597611598821245 24 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Nagpa'>Nagpa</a> +Bmp1 2.83284622628297 0.517967853857585 4.09387916064743 0.00107217035218767 0.00661268309106014 -0.708641495529353 39 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Bmp1'>Bmp1</a> +Crem 2.33712898304139 -0.121515515943567 4.0829392931282 0.00109547464985413 0.00672008911550302 -0.694023102630085 16 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Crem'>Crem</a> +AI506816 2.42270659752045 -0.452690836228738 4.06592993902701 0.00113274010846169 0.00690883244123217 -0.71823549330855 12 <a href='http://www.genecards.org/index.php?path=/Search/keyword/AI506816'>AI506816</a> +Snhg12 1.2392736392255 8.22309194102909 4.06341770887408 0.0011383527598174 0.00690883244123217 -1.46153826275546 5403 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snhg12'>Snhg12</a> +Snord99 1.60658132000619 7.61494864267921 4.05085172286681 0.00116685579559478 0.00702317443883207 -1.44229619547632 3970 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord99'>Snord99</a> +Mir450b -1.85261764183761 3.54483087111489 -4.0485135276699 0.00117223928473074 0.00702317443883207 -1.03659851317493 205 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir450b'>Mir450b</a> +Mir218-1 -2.37943795492075 -0.788253108012747 -4.04703416313971 0.00117565847310861 0.00702317443883207 -0.747038393026922 7 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir218-1'>Mir218-1</a> +Mir140 -0.901201558594089 9.41159056411459 -4.03552071597731 0.00120261909580773 0.00711569212542235 -1.59661829698077 10795 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir140'>Mir140</a> +Mir483 -2.42347249247516 -0.756810762138252 -4.03017784461274 0.0012153437165189 0.00711569212542235 -0.779102255351839 7 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir483'>Mir483</a> +Sqrdl 3.73159563362893 0.945260485192632 4.02973478085716 0.00121640506624817 0.00711569212542235 -0.861776345505721 102 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Sqrdl'>Sqrdl</a> +Mir144 -2.29129119700542 9.41554506116587 -4.02892270273821 0.00121835283652175 0.00711569212542235 -1.60506726133582 13709 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir144'>Mir144</a> +Mir210 -1.50896749399836 4.99944311707418 -4.02726966499444 0.00122232748166764 0.00711569212542235 -1.27568646998696 592 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir210'>Mir210</a> +Mir136 -1.91584100290298 5.18425364003902 -4.01919516322722 0.00124193308478254 0.0071567962107923 -1.30273093425232 753 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir136'>Mir136</a> +Mir3071 -1.91584100290298 5.18425364003902 -4.01919516322722 0.00124193308478254 0.0071567962107923 -1.30273093425232 753 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3071'>Mir3071</a> +Snord43 1.12653255459757 7.42275234629614 4.00820447995329 0.00126913582767258 0.00727680391645436 -1.51733899954002 2975 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord43'>Snord43</a> +Nlrp5-ps 3.06966395518949 -0.135132312387713 3.98319245863032 0.00133332885542151 0.00760664112017971 -0.902428549559341 34 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Nlrp5-ps'>Nlrp5-ps</a> +4833418N02Rik 1.82386047796749 3.16360132579728 3.94914311648112 0.00142607040510993 0.00809525538423099 -1.16130756295351 170 <a href='http://www.genecards.org/index.php?path=/Search/keyword/4833418N02Rik'>4833418N02Rik</a> +Pknox1 2.58217103686749 -0.386376496641391 3.94009175499237 0.00145181139000837 0.00820057819801758 -0.95836656931183 16 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Pknox1'>Pknox1</a> +Mir1843 1.0607275776375 7.37281183848222 3.92128643575477 0.00150681377235572 0.008458947103908 -1.6871582740604 2782 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1843'>Mir1843</a> +Scarna3b 1.05890367361984 7.37450114126396 3.91942250502631 0.00151237967501948 0.008458947103908 -1.69099763322655 2784 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Scarna3b'>Scarna3b</a> +Phyhd1 2.69871613662387 -0.324381809808589 3.91199503566496 0.00153476742516205 0.00850676625406398 -1.01680363882686 20 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Phyhd1'>Phyhd1</a> +Gm14207 -2.37304409257741 -0.416502509079365 -3.91164184680055 0.00153584035787658 0.00850676625406398 -1.00193629125355 11 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm14207'>Gm14207</a> +2700038G22Rik -1.20941383309973 5.69714561045198 -3.89423392377302 0.00158967928624185 0.00876243509952633 -1.61494260853442 872 <a href='http://www.genecards.org/index.php?path=/Search/keyword/2700038G22Rik'>2700038G22Rik</a> +Mir1249 -1.57997335358757 3.92571996538164 -3.86749708921129 0.00167613304205796 0.00914790116608117 -1.45071018307216 240 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1249'>Mir1249</a> +Mir680-2 2.69993600843854 2.33940488575521 3.86630244603638 0.00168010559076576 0.00914790116608117 -1.19260507987069 134 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir680-2'>Mir680-2</a> +4732471J01Rik 2.47123788102083 1.83426864599497 3.86203852417355 0.00169436257731633 0.00914790116608117 -1.16621943210526 78 <a href='http://www.genecards.org/index.php?path=/Search/keyword/4732471J01Rik'>4732471J01Rik</a> +0610005C13Rik 3.75552246080227 1.36486301235638 3.86197876879019 0.00169456324819645 0.00914790116608117 -1.18181214765895 126 <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610005C13Rik'>0610005C13Rik</a> +Mir297a-3 -2.83038541581836 0.620898493219045 -3.86045228910567 0.00169969767502998 0.00914790116608117 -1.12583690632738 32 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir297a-3'>Mir297a-3</a> +D830015G02Rik -2.85288965105576 -0.0430116131169372 -3.8540007067199 0.00172157316996324 0.00918761905215916 -1.135758525707 19 <a href='http://www.genecards.org/index.php?path=/Search/keyword/D830015G02Rik'>D830015G02Rik</a> +Mir190b -2.58480150088673 0.118920372323834 -3.85352956525721 0.00172318183800356 0.00918761905215916 -1.12342997930169 19 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir190b'>Mir190b</a> +Cacnb2 -2.36615720731133 -0.788253108012747 -3.84657108578939 0.00174711947070295 0.00927192240033519 -1.12169301350773 7 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Cacnb2'>Cacnb2</a> +Mtfr1 2.77427419358368 0.492589466798896 3.83997888411189 0.001770108543009 0.00935043447950588 -1.18729669638225 40 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mtfr1'>Mtfr1</a> +Snord1a 1.56162899910724 3.64400301591315 3.83681604346118 0.0017812471515648 0.00936313497745819 -1.45598973323054 230 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord1a'>Snord1a</a> +Snord68 0.957663081634941 8.79334935483305 3.83464756418373 0.00178892500007527 0.00936313497745819 -1.95644313626433 7303 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord68'>Snord68</a> +Mir878 2.41936085459412 -0.447944854953861 3.82652263259005 0.00181799260036803 0.00947182446127819 -1.16702401112308 13 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir878'>Mir878</a> +Mir511 1.70981318188926 3.27929603694437 3.81643804724114 0.0018547387918105 0.00959956329857923 -1.44128807747474 183 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir511'>Mir511</a> +Gm15787 2.48153800186339 -0.386376496641391 3.81519042194731 0.00185933697544786 0.00959956329857923 -1.19313192146596 14 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm15787'>Gm15787</a> +Surf1 2.36126838851735 0.0872159088448913 3.80305260835126 0.00190467958178741 0.00978936667936682 -1.23097217655323 20 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Surf1'>Surf1</a> +Mir1968 2.37800084613411 0.673754504632647 3.77926083620018 0.00199683807660974 0.0102052996591412 -1.28734965758831 33 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1968'>Mir1968</a> +0610007N19Rik -1.90120438734532 2.49555567542219 -3.77758577340756 0.00200349441161053 0.0102052996591412 -1.41487533930946 104 <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610007N19Rik'>0610007N19Rik</a> +Snhg8 1.59039445480745 3.20715500905903 3.75615085858512 0.00209068421652196 0.0106020919602291 -1.55245580151111 164 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snhg8'>Snhg8</a> +Mir99b -1.91682795135645 10.9172256229833 -3.75211079306552 0.0021075435523792 0.0106402973153304 -2.25375326353787 35086 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir99b'>Mir99b</a> +Mir365-2 2.40700496454038 0.263026808334256 3.74756102414217 0.00212669484901157 0.0106896864437102 -1.33894003797924 25 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir365-2'>Mir365-2</a> +A630019I02Rik -2.46429396746277 -0.331334129436178 -3.72894212518103 0.00220692150206125 0.0110442869905785 -1.34913426897275 12 <a href='http://www.genecards.org/index.php?path=/Search/keyword/A630019I02Rik'>A630019I02Rik</a> +Snora24 1.55151202645698 3.18622291582758 3.72443395692917 0.00222680324291416 0.011095120088057 -1.61270421930364 160 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora24'>Snora24</a> +Tmem205 3.35434252485109 1.34402776298411 3.71826658220279 0.00225429637910924 0.0111803962803989 -1.43852442151233 106 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Tmem205'>Tmem205</a> +Chka 2.66265038819564 -0.367431606769972 3.71621547263374 0.00226351581136911 0.0111803962803989 -1.38147433178837 20 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Chka'>Chka</a> +Il15ra 3.0322333836799 1.34537734368953 3.69802409752219 0.00234697158113459 0.0115426490261835 -1.46743653610507 78 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Il15ra'>Il15ra</a> +Mir340 1.08524047523296 8.40150339094243 3.68614126686871 0.00240316001921397 0.0117592747718197 -2.22640527546981 5906 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir340'>Mir340</a> +Mir222 -0.989531454809674 6.83748363675873 -3.68437434098812 0.00241163040894463 0.0117592747718197 -2.12318215364121 1840 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir222'>Mir222</a> +Snord16a 2.29129601947442 3.76378890459482 3.66271871458069 0.0025179297139219 0.0122253523556804 -1.78739319047154 368 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord16a'>Snord16a</a> +Snora16a 1.52372874357926 4.55536943029929 3.65510898252504 0.0025563971250754 0.0123595301682671 -1.93830245300744 464 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora16a'>Snora16a</a> +Meg3 -2.68467060880573 -0.63693223477029 -3.65193847372806 0.00257259886012651 0.0123853810101449 -1.49159048882037 12 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Meg3'>Meg3</a> +Mir503 -1.62803161355467 2.50957996141068 -3.64484640281096 0.00260921685489431 0.0125088925690521 -1.68081269699905 88 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir503'>Mir503</a> +Snord34 1.9527050627559 2.43578559807808 3.64115899694926 0.00262846334208935 0.0125484379636985 -1.64754683241552 110 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord34'>Snord34</a> +Mir330 -1.20046349365495 3.89404790732931 -3.62347773804946 0.00272276191759244 0.0129444639498874 -1.93549975651123 231 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir330'>Mir330</a> +Snord123 -1.85009039423829 2.46689582455698 -3.62068933774574 0.00273794187669866 0.012962621084287 -1.71578244093404 102 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord123'>Snord123</a> +1700123M08Rik -2.53907013725051 -0.265019789848831 -3.61128151512854 0.0027897908425338 0.0131535179807069 -1.57539508080877 14 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1700123M08Rik'>1700123M08Rik</a> +U05342 2.83058680402627 0.79675702914225 3.60519476819122 0.00282386325723748 0.0132525688403876 -1.63602002228639 54 <a href='http://www.genecards.org/index.php?path=/Search/keyword/U05342'>U05342</a> +Mir331 -1.23366463697674 4.50384654608554 -3.60339313514846 0.00283402874413198 0.0132525688403876 -2.05839651689923 359 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir331'>Mir331</a> +Snord47 1.75254142711948 3.676071658915 3.56574123782182 0.00305512804060726 0.014228167731971 -1.9866272780716 277 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord47'>Snord47</a> 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href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3096b'>Mir3096b</a> +Snord93 -1.20474634794453 4.70053095823646 -3.5153757202842 0.00337831126227612 0.0153571838655659 -2.25812559332021 435 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord93'>Snord93</a> +Adhfe1 2.52527478072387 0.179068747865736 3.50530102423767 0.00344697804598443 0.0156071505970962 -1.80634560509756 25 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Adhfe1'>Adhfe1</a> +Gm10768 3.5358301921593 0.021906952859762 3.48225041539546 0.00360941220951063 0.0162780210713503 -1.87207612241023 59 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm10768'>Gm10768</a> +Snord85 1.10352244207212 9.7813263715169 3.47953980186612 0.00362901230761682 0.0163019804842157 -2.72788678002978 15092 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord85'>Snord85</a> +AF357399 1.79554087095325 2.33898958600026 3.47297259387192 0.00367694357668826 0.0164098488394083 -1.96818697726206 89 <a href='http://www.genecards.org/index.php?path=/Search/keyword/AF357399'>AF357399</a> +Mir551b 2.15397612089142 -0.590132795422603 3.47231349486416 0.00368178904722922 0.0164098488394083 -1.82422890137775 10 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir551b'>Mir551b</a> +Def8 2.41874321422316 -0.465993593620758 3.46859651584658 0.00370923535603452 0.0164678503550015 -1.83970905317218 16 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Def8'>Def8</a> +Mir664 -1.01764634401405 5.37432688059702 -3.45211961435443 0.00383339754528852 0.0168755824717367 -2.46240607108039 632 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir664'>Mir664</a> +Mir467c 2.31849317866793 0.658275206086465 3.45045370722881 0.00384618107849534 0.0168755824717367 -1.9100187677291 35 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir467c'>Mir467c</a> +Mir345 -0.912671478268366 6.07047283018279 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href='http://www.genecards.org/index.php?path=/Search/keyword/Mir98'>Mir98</a> +4930483K19Rik 2.52533407356931 -0.00211602021024845 3.38443072134124 0.00438878944604477 0.0185466991034707 -2.0252331979185 24 <a href='http://www.genecards.org/index.php?path=/Search/keyword/4930483K19Rik'>4930483K19Rik</a> +9530036O11Rik -2.18021083734 -0.880373807283523 -3.36944259471363 0.00452229090218708 0.0190403465660349 -2.01615459630653 6 <a href='http://www.genecards.org/index.php?path=/Search/keyword/9530036O11Rik'>9530036O11Rik</a> +Airn -3.32728005388875 1.05242623359369 -3.36289553627823 0.00458187540512432 0.0192202935192899 -2.09508526477381 66 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Airn'>Airn</a> +Mir542 -1.22316159239699 3.81531438686763 -3.32742457590211 0.00491862125207608 0.0205573144638052 -2.50522353523098 225 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir542'>Mir542</a> +Mir350 -1.56832295120394 3.2654986223895 -3.31591379494715 0.00503313311490562 0.0209591419128004 -2.43484812644587 172 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir350'>Mir350</a> +Mir467d -2.52245592103549 0.453062661337275 -3.31293337335217 0.00506321480472689 0.0210077385170668 -2.14396740548906 27 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir467d'>Mir467d</a> +Gm10069 5.68607477678649 3.08099524867498 3.3046846231052 0.00514741011835455 0.0212796918298643 -2.27892670543982 1309 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm10069'>Gm10069</a> +Wwp1 3.00070653341197 1.74135246228108 3.28733760371041 0.00532906211683886 0.0219415999009116 -2.26148023738523 118 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Wwp1'>Wwp1</a> +Mir431 -2.52814898361935 0.729842447535775 -3.28575204794379 0.0053459813956647 0.0219415999009116 -2.20212311657876 36 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir431'>Mir431</a> +1810058I24Rik 2.62271409770273 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href='http://www.genecards.org/index.php?path=/Search/keyword/Mir92b'>Mir92b</a> +Gm16157 2.66162389621631 -0.365224948706732 3.20356821793981 0.00630038071552899 0.0253124450578119 -2.34859094591427 22 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm16157'>Gm16157</a> +Snord19 0.841113010089355 7.11055248976838 3.19415039125178 0.00642005717801694 0.0257027552284819 -3.11414489267883 2203 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord19'>Snord19</a> +Schip1 -2.57567954952992 -0.153384190338395 -3.18549465102036 0.00653204236936578 0.0260045455633494 -2.38778174828683 17 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Schip1'>Schip1</a> +Snord69 0.84304704580235 7.14897332827513 3.18307678347552 0.00656366958087888 0.0260045455633494 -3.13872359988574 2301 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord69'>Snord69</a> +Mir3061 -1.52813229940924 2.87430787227175 -3.18306594661466 0.00656381167593746 0.0260045455633494 -2.63327753238114 119 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3061'>Mir3061</a> +Mir29a -0.877942320051101 11.0487374837586 -3.17676979444805 0.00664688724206556 0.0262425548207502 -3.41112827127731 33081 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir29a'>Mir29a</a> +Gm10319 2.14644292502742 -0.590132795422603 3.17164218489659 0.00671531580422408 0.0264212942504127 -2.38832170685348 12 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm10319'>Gm10319</a> +Mir127 -1.25650791022161 9.78648771687729 -3.16887488380797 0.00675253616433696 0.0264764390498573 -3.34593460449095 14429 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir127'>Mir127</a> +B330016D10Rik -1.92161264416092 -0.63693223477029 -3.1657281651115 0.0067951088367248 0.0264822665438203 -2.39563418410943 8 <a href='http://www.genecards.org/index.php?path=/Search/keyword/B330016D10Rik'>B330016D10Rik</a> +Eci2 3.49526347553937 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href='http://www.genecards.org/index.php?path=/Search/keyword/Snord49b'>Snord49b</a> +G630025P09Rik 2.04699188377197 -0.244188556172649 3.10780445430196 0.00762812710513572 0.0292070235804022 -2.51605087870259 15 <a href='http://www.genecards.org/index.php?path=/Search/keyword/G630025P09Rik'>G630025P09Rik</a> +Mir329 -2.25038749201629 0.143148280966294 -3.10219089596341 0.00771405119681339 0.0294372321590772 -2.52468319230879 18 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir329'>Mir329</a> +Gm5105 -2.16408947287434 -0.894252721332116 -3.09357723434137 0.00784776462691287 0.029847664797692 -2.53204083131101 7 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm5105'>Gm5105</a> +1700001L05Rik 2.36321176153954 -0.504303555595595 3.08655241783997 0.00795851133538617 0.0301683104108825 -2.55344737484833 16 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1700001L05Rik'>1700001L05Rik</a> +Snord2 0.691526499495304 8.00175923757187 3.08142494474571 0.008040321980135 0.030265949526277 -3.40026204758547 3954 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord2'>Snord2</a> +Mir22 -0.847615802202714 16.7326675324719 -3.08005897908952 0.00806225653232276 0.030265949526277 -3.96615097802407 1751447 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir22'>Mir22</a> +Mir22hg -0.847524583315551 16.7327250619969 -3.07996011844832 0.00806384632426661 0.030265949526277 -3.96634849509949 1751491 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir22hg'>Mir22hg</a> +1700012B15Rik 2.2557460290944 -0.13987829366259 3.07437268195085 0.00815420485488848 0.0305047466866484 -2.59032088872728 19 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1700012B15Rik'>1700012B15Rik</a> +Mir185 -1.40702024721662 4.08694622913669 -3.05877067430607 0.008411855287644 0.0313657741281105 -3.06664608794292 331 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir185'>Mir185</a> +Slc25a44 2.21491041672761 1.66497498687079 3.04421973608031 0.00865939699909311 0.032183622071548 -2.71149512021232 77 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Slc25a44'>Slc25a44</a> +Mir495 -1.8776791373757 -0.650811148818883 -3.04203753845606 0.00869713645483206 0.0322189373213097 -2.62552265945633 7 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir495'>Mir495</a> +Sec16b 3.05043595272399 0.157027195014887 3.02828873074633 0.00893867714364734 0.0330065715886784 -2.71905679017603 57 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Sec16b'>Sec16b</a> +Mir152 -0.718432101776587 7.28616446583531 -3.01300789436766 0.00921491113521454 0.0339168180815477 -3.48441058966127 2398 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir152'>Mir152</a> +Snora3 2.07140605143005 1.76186432056615 3.0107219189642 0.00925695325975535 0.0339620053677841 -2.78114890188917 69 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora3'>Snora3</a> +2010003O02Rik 1.94956844186534 -0.0201000379109987 2.97528778647613 0.00993335310087066 0.0362443709129751 -2.76683258555442 17 <a href='http://www.genecards.org/index.php?path=/Search/keyword/2010003O02Rik'>2010003O02Rik</a> +Mir704 1.80973957230357 -0.756810762138252 2.9728569191809 0.00998150161417436 0.0362443709129751 -2.75225460174575 7 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir704'>Mir704</a> +D130020L05Rik 2.51176492481985 1.19972413900365 2.97271570851407 0.00998430564726682 0.0362443709129751 -2.82735067383733 52 <a href='http://www.genecards.org/index.php?path=/Search/keyword/D130020L05Rik'>D130020L05Rik</a> +Mir3076 -2.06400546664394 -0.027699510367659 -2.97161874120075 0.0100061146692262 0.0362443709129751 -2.75226107651724 17 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3076'>Mir3076</a> +Mirlet7c-1 -0.837889959835657 5.12475158025001 -2.96511158812865 0.0101364526370322 0.0366002925913093 -3.39152169935695 536 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mirlet7c-1'>Mirlet7c-1</a> +Mir540 -2.19546334412823 0.490670971257216 -2.96107695486126 0.0102181042879641 0.0367787286831769 -2.78918578498352 25 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir540'>Mir540</a> +Mir1947 -1.28776936588478 3.27191581050928 -2.95683139992983 0.0103047236916254 0.0369738670822157 -3.13442994008256 146 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1947'>Mir1947</a> +9130019P16Rik 2.19950155178161 0.0491090861538386 2.93627487051494 0.0107344511680762 0.0383950118582288 -2.85952778968786 20 <a href='http://www.genecards.org/index.php?path=/Search/keyword/9130019P16Rik'>9130019P16Rik</a> +Mir5121 1.92484055344077 0.963995516493567 2.91681375354519 0.0111574945019998 0.0397834413336931 -2.90528656811773 37 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir5121'>Mir5121</a> +B430319G15Rik -1.98479980231837 -0.986373420602892 -2.90027155266244 0.0115299314828684 0.0408786538511516 -2.88966321680022 6 <a href='http://www.genecards.org/index.php?path=/Search/keyword/B430319G15Rik'>B430319G15Rik</a> +Mir351 -0.833417329407842 8.58289887759314 -2.89999295816495 0.0115363072217974 0.0408786538511516 -3.79447142137588 5692 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir351'>Mir351</a> +D330050I16Rik 1.78527438588565 -0.392012482832458 2.89505348884379 0.0116499250396066 0.0411534503721088 -2.89805092182303 11 <a href='http://www.genecards.org/index.php?path=/Search/keyword/D330050I16Rik'>D330050I16Rik</a> +BC024386 2.76807972012068 -0.350592172752806 2.88853915590151 0.0118014481853742 0.0415600382083702 -2.93769383343029 35 <a href='http://www.genecards.org/index.php?path=/Search/keyword/BC024386'>BC024386</a> +Mir666 -2.07579086945099 -0.498012096151827 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href='http://www.genecards.org/index.php?path=/Search/keyword/Mir449a'>Mir449a</a> +Ncaph2 2.43172128495717 0.531053368370468 2.81514840260429 0.0136477529969634 0.0464838393120456 -3.10990472720523 39 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Ncaph2'>Ncaph2</a> +Tmem41a 2.13366400352273 -0.61462282166951 2.81019216927593 0.0137821511685655 0.0468018883432536 -3.05559526679725 14 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Tmem41a'>Tmem41a</a> +Mir337 -2.00512882554678 1.46245475734951 -2.790176090596 0.0143381997019222 0.0484912300051582 -3.15685281038144 50 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir337'>Mir337</a> +E430016F16Rik -1.97871005920294 -0.986373420602892 -2.78924386549867 0.0143646237876805 0.0484912300051582 -3.09307014868296 6 <a href='http://www.genecards.org/index.php?path=/Search/keyword/E430016F16Rik'>E430016F16Rik</a> +1700003F17Rik -2.01422348895548 0.00986412853889808 -2.78534021594328 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href='http://www.genecards.org/index.php?path=/Search/keyword/Gm16119'>Gm16119</a> +2010308F09Rik -1.83277349898908 -0.650811148818883 -2.73961897562678 0.0158419025113795 0.0517925809899256 -3.18111223859539 7 <a href='http://www.genecards.org/index.php?path=/Search/keyword/2010308F09Rik'>2010308F09Rik</a> +Gm8883 2.16409799450603 -0.590132795422603 2.72505563686563 0.0163028203034417 0.0529872269292577 -3.21224705829732 16 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm8883'>Gm8883</a> +Zfp862 2.16409799450603 -0.590132795422603 2.72505563686563 0.0163028203034417 0.0529872269292577 -3.21224705829732 16 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Zfp862'>Zfp862</a> +Snhg7 1.72599658448324 2.92713305382255 2.72369233450925 0.0163466291666071 0.0529872269292577 -3.48946421579912 173 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snhg7'>Snhg7</a> +B830017H08Rik -2.23343112594958 -0.833574367935836 -2.72209538930301 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href='http://www.genecards.org/index.php?path=/Search/keyword/Mir338'>Mir338</a> +Snord12 0.862355865323009 7.21183801132978 2.69866680699734 0.017171427527834 0.0546270939470388 -4.08039835847175 2566 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord12'>Snord12</a> +Gm16551 1.95751791415313 -0.691386427467094 2.69401162790859 0.0173292489773132 0.0546270939470388 -3.26351851959596 11 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm16551'>Gm16551</a> +Mir1938 -1.6694250746775 -1.13917247326995 -2.69395153729379 0.0173312953626889 0.0546270939470388 -3.27380411394135 4 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1938'>Mir1938</a> +Mir384 -1.6694250746775 -1.13917247326995 -2.69395153729379 0.0173312953626889 0.0546270939470388 -3.27380411394135 4 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir384'>Mir384</a> +Sec14l1 -1.6694250746775 -1.13917247326995 -2.69395153729379 0.0173312953626889 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href='http://www.genecards.org/index.php?path=/Search/keyword/Hsf4'>Hsf4</a> +9530026P05Rik -2.07695780402641 0.308348068257344 -2.63023447836339 0.0196382434958373 0.0602345049159956 -3.38900744489907 20 <a href='http://www.genecards.org/index.php?path=/Search/keyword/9530026P05Rik'>9530026P05Rik</a> +F730035M05Rik 1.78278284441709 0.0460524556882713 2.60073804597223 0.0208042043193282 0.0636396705853981 -3.45006336955945 17 <a href='http://www.genecards.org/index.php?path=/Search/keyword/F730035M05Rik'>F730035M05Rik</a> +4931440P22Rik 1.81357503948527 -0.34669122290937 2.59692706678062 0.0209596355730796 0.0639437010397962 -3.44244562957201 12 <a href='http://www.genecards.org/index.php?path=/Search/keyword/4931440P22Rik'>4931440P22Rik</a> +Mir300 -1.68375330243594 3.41000156536173 -2.5819475209075 0.0215814969001033 0.0656653012347144 -3.85223959755949 222 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir300'>Mir300</a> +Gm9961 1.6141478502722 -0.484133182103234 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href='http://www.genecards.org/index.php?path=/Search/keyword/St7l'>St7l</a> +Snord88c 0.793290174312999 4.47693446317466 2.50505317099491 0.0250634970146661 0.0740866582739222 -4.17079027962479 341 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord88c'>Snord88c</a> +9330175M20Rik -1.65022439160042 -0.360570136957963 -2.50294066783667 0.0251663831454311 0.0741985611600436 -3.59490203212403 9 <a href='http://www.genecards.org/index.php?path=/Search/keyword/9330175M20Rik'>9330175M20Rik</a> +Snora52 1.11047151370588 2.69319347264049 2.50050576985066 0.0252854729408082 0.0742992649502222 -3.88083546486857 105 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora52'>Snora52</a> +4933405D12Rik 2.28373557503359 -0.125999379613997 2.49952793100309 0.0253334503629621 0.0742992649502222 -3.64207314883416 26 <a href='http://www.genecards.org/index.php?path=/Search/keyword/4933405D12Rik'>4933405D12Rik</a> +Mir188 -1.84047092737597 1.30222680574037 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href='http://www.genecards.org/index.php?path=/Search/keyword/Crebzf'>Crebzf</a> +AW495222 3.12693001673928 0.217900170575655 2.46889622052332 0.0268812784562901 0.0766788467965674 -3.7522647303971 101 <a href='http://www.genecards.org/index.php?path=/Search/keyword/AW495222'>AW495222</a> +Lrrc28 2.42525008262091 0.708273211214943 2.46119616740811 0.0272843555867779 0.077634537966368 -3.75212597460025 60 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Lrrc28'>Lrrc28</a> +Mir3086 -1.56502610075238 0.163979514642475 -2.45070863513763 0.0278426426188866 0.079026008030223 -3.67658416235536 15 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3086'>Mir3086</a> +Gm16548 1.56554530187766 -0.880373807283523 2.43719245534725 0.028578244472197 0.0809125978728953 -3.7171315266521 6 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm16548'>Gm16548</a> +Vsig8 0.720909981822672 5.46827442991139 2.4297652846464 0.0289903098093856 0.081876097753735 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href='http://www.genecards.org/index.php?path=/Search/keyword/4930412C18Rik'>4930412C18Rik</a> +Gm17769 -1.71539919467515 -1.13917247326995 -2.36022700442918 0.0331324488036802 0.0902246398210002 -3.86472183787187 4 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm17769'>Gm17769</a> +Fth1 2.86103494155137 3.45595627169968 2.35821583980086 0.033260223411433 0.0903569402677262 -4.19586341531867 625 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Fth1'>Fth1</a> +4833417C18Rik 1.47974694653215 -0.544811535499514 2.35068477635695 0.0337428496416542 0.0914503359646734 -3.86474671238307 9 <a href='http://www.genecards.org/index.php?path=/Search/keyword/4833417C18Rik'>4833417C18Rik</a> +Snora61 0.958904821800182 3.29767563160608 2.349125503029 0.0338436003101147 0.0915060378053102 -4.26190631619714 164 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora61'>Snora61</a> +Mirlet7f-2 0.650708366569944 9.71888537299185 2.34186730999564 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href='http://www.genecards.org/index.php?path=/Search/keyword/Ankrd10'>Ankrd10</a> +9330179D12Rik -1.85045093530144 1.28320177813767 -2.31096269706071 0.0363999711565358 0.0970382408635685 -3.9951686511153 40 <a href='http://www.genecards.org/index.php?path=/Search/keyword/9330179D12Rik'>9330179D12Rik</a> +Snora62 1.7847261774294 -0.244188556172649 2.29775908931167 0.0373260968205211 0.0992752365319687 -3.96525604386916 17 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora62'>Snora62</a> +BC024582 1.59980554588654 -0.452690836228738 2.2959268866433 0.0374563520512198 0.0993899946289343 -3.96118314063755 10 <a href='http://www.genecards.org/index.php?path=/Search/keyword/BC024582'>BC024582</a> +Gm10804 1.52979741848186 -0.355824155683085 2.29375082460336 0.0376116093012649 0.0994728784445405 -3.96360070348265 12 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm10804'>Gm10804</a> +Mir1195 1.10164801174588 3.09590694872149 2.29304709119496 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href='http://www.genecards.org/index.php?path=/Search/keyword/0610009L18Rik'>0610009L18Rik</a> +Snhg3 1.25378785890833 2.38956644178022 2.26464378812804 0.0397474393896485 0.103777261528111 -4.23895965644335 94 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snhg3'>Snhg3</a> +Mir297-2 1.46684984163613 1.40872493183085 2.26345073111919 0.0398373712088629 0.103777261528111 -4.09858373085422 47 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir297-2'>Mir297-2</a> +Etfb 2.40847795385732 0.265851908477543 2.26169079632117 0.0399703828812269 0.103886576007927 -4.07904638296427 53 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Etfb'>Etfb</a> +Mir708 -1.85451172422601 -0.280376883322022 -2.25778324055568 0.0402671991288784 0.104420168650114 -4.0216739515904 16 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir708'>Mir708</a> +Rchy1 1.62884124887726 -0.438811922180145 2.25361813300649 0.0405858566094605 0.105007851227652 -4.03354975134699 11 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rchy1'>Rchy1</a> +A730056A06Rik -1.68694694851363 -1.13917247326995 -2.24683042206407 0.0411102355769964 0.105912931059682 -4.05854864097368 6 <a href='http://www.genecards.org/index.php?path=/Search/keyword/A730056A06Rik'>A730056A06Rik</a> +4933406I18Rik 1.77699338800155 -0.768738207773087 2.24668779416224 0.0411213220503411 0.105912931059682 -4.04580334564085 11 <a href='http://www.genecards.org/index.php?path=/Search/keyword/4933406I18Rik'>4933406I18Rik</a> +Mir134 -1.97599424729025 0.963837048223167 -2.23531953342299 0.0420140490275288 0.107968535901825 -4.10273890592774 40 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir134'>Mir134</a> +0610040F04Rik 1.48024531718237 -0.126261497218445 2.21863530367332 0.0433571530862421 0.111169689149219 -4.09406770500723 13 <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610040F04Rik'>0610040F04Rik</a> +Hyi 1.7208723887239 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href='http://www.genecards.org/index.php?path=/Search/keyword/Pglyrp2'>Pglyrp2</a> +R74862 1.46156334047426 0.026537555448611 2.13628776933242 0.0505936418662866 0.124144828751469 -4.22999882095606 15 <a href='http://www.genecards.org/index.php?path=/Search/keyword/R74862'>R74862</a> +Snora28 1.12037820753744 2.12526039705926 2.12930512434667 0.0512562751008916 0.125500879592526 -4.42817337501701 71 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora28'>Snora28</a> +Cd40 -1.37088395935442 -1.27661443246381 -2.12752810799839 0.0514261885899383 0.125647283043083 -4.27058401928142 4 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Cd40'>Cd40</a> +Mug-ps1 2.13180518001054 -0.635454055345691 2.12264061264248 0.0518962135703567 0.126524742914053 -4.25630236233275 31 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mug-ps1'>Mug-ps1</a> +A630072M18Rik 1.38270587147115 0.396971820945472 2.11893446805287 0.0522552789377958 0.127117232913158 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href='http://www.genecards.org/index.php?path=/Search/keyword/B230206H07Rik'>B230206H07Rik</a> +Snord55 0.601021636432394 6.97866331241363 2.08546096371218 0.0556040229210925 0.132208091094402 -5.17041448286456 2070 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord55'>Snord55</a> +Ralgps2 1.88483656314977 0.227262055965901 2.08532736079326 0.0556177771475135 0.132208091094402 -4.34269584383277 30 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Ralgps2'>Ralgps2</a> +Mir33 0.994045785258037 2.79490734914157 2.08206634259786 0.055954469010935 0.132731910897041 -4.63235497043256 118 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir33'>Mir33</a> +Mir26a-1 -0.807612985022876 4.30478785875254 -2.07928199044436 0.0562434329588863 0.13314057470143 -4.90515725875701 302 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir26a-1'>Mir26a-1</a> +Gm16845 1.58909272532801 0.693110936601907 2.07661019420121 0.0565220086427535 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href='http://www.genecards.org/index.php?path=/Search/keyword/A930005H10Rik'>A930005H10Rik</a> +C920021L13Rik 1.45659708523928 0.785774819657178 1.89280562125827 0.0790163750358231 0.171402440904704 -4.64971051817534 32 <a href='http://www.genecards.org/index.php?path=/Search/keyword/C920021L13Rik'>C920021L13Rik</a> +4931403E22Rik 1.70378545689415 -0.814059467696176 1.88880372983809 0.079585814935806 0.172310085088719 -4.62498282958674 16 <a href='http://www.genecards.org/index.php?path=/Search/keyword/4931403E22Rik'>4931403E22Rik</a> +Mir1964 -0.871113074799274 2.86663339631991 -1.88648279477582 0.0799177575555235 0.172701063202372 -4.9744960348716 105 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1964'>Mir1964</a> +2410004N09Rik 2.12780696213311 -0.132941404588628 1.87600039224749 0.0814325355366182 0.175611886412351 -4.66535335652261 50 <a href='http://www.genecards.org/index.php?path=/Search/keyword/2410004N09Rik'>2410004N09Rik</a> +4930545L23Rik 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href='http://www.genecards.org/index.php?path=/Search/keyword/Snord17'>Snord17</a> +2700089E24Rik 1.9346637528719 0.708144926037837 1.59009813142159 0.13389606984202 0.248415310064625 -5.10719912908875 70 <a href='http://www.genecards.org/index.php?path=/Search/keyword/2700089E24Rik'>2700089E24Rik</a> +1300002E11Rik 1.66663408255978 -0.437333742755547 1.58582291431296 0.134863747546901 0.249804441478919 -5.0690582710292 28 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1300002E11Rik'>1300002E11Rik</a> +4930474G06Rik -1.090892671974 -1.03317285995058 -1.58193904835456 0.135748030192849 0.250441466610603 -5.09374604062072 4 <a href='http://www.genecards.org/index.php?path=/Search/keyword/4930474G06Rik'>4930474G06Rik</a> +A430093F15Rik -1.090892671974 -1.03317285995058 -1.58193904835456 0.135748030192849 0.250441466610603 -5.09374604062072 4 <a href='http://www.genecards.org/index.php?path=/Search/keyword/A430093F15Rik'>A430093F15Rik</a> +Rreb1 1.35338804346774 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href='http://www.genecards.org/index.php?path=/Search/keyword/1700034P13Rik'>1700034P13Rik</a> +Fam120aos 1.03573302470771 -1.13917247326995 1.5706655582452 0.138342934232158 0.251258367802273 -5.09634899411597 4 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Fam120aos'>Fam120aos</a> +1700102H20Rik -1.01261850877746 -1.42941348513087 -1.56975595848976 0.138554138577694 0.251258367802273 -5.13526440107113 4 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1700102H20Rik'>1700102H20Rik</a> +9230112J17Rik -1.01261850877746 -1.42941348513087 -1.56975595848976 0.138554138577694 0.251258367802273 -5.13526440107113 4 <a href='http://www.genecards.org/index.php?path=/Search/keyword/9230112J17Rik'>9230112J17Rik</a> +Mir3100 -1.01261850877746 -1.42941348513087 -1.56975595848976 0.138554138577694 0.251258367802273 -5.13526440107113 4 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3100'>Mir3100</a> +Mir294 1.03626141233244 -1.13917247326995 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href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3069'>Mir3069</a> +Snord87 0.414265796353463 6.8857147404585 1.55208332473347 0.142712543117168 0.255227291060641 -5.99741848701943 1759 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord87'>Snord87</a> +4932702P03Rik 1.50538536018542 -0.190947829244951 1.54735549642484 0.143842852742846 0.256846158027523 -5.12545513466049 20 <a href='http://www.genecards.org/index.php?path=/Search/keyword/4932702P03Rik'>4932702P03Rik</a> +Mir341 -1.11910417431075 -0.268449437687187 -1.54504024071338 0.144399143660684 0.257436598307563 -5.09444510471904 10 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir341'>Mir341</a> +Fam19a2 -1.08108870526458 -1.03317285995058 -1.54274205574173 0.144953138847169 0.258021109866802 -5.14743110946704 4 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Fam19a2'>Fam19a2</a> +Mir2137 -1.25397648150412 -0.986373420602892 -1.53902949676667 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href='http://www.genecards.org/index.php?path=/Search/keyword/Mir672'>Mir672</a> +Mir20a -0.370723568916546 5.31004708857036 -1.04192548554098 0.314918543938074 0.455414522982691 -6.48442003496676 643 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir20a'>Mir20a</a> +0610043K17Rik 0.984989107300095 0.566661427402775 1.03734276139365 0.316975604930417 0.457287012691463 -5.71838241477771 32 <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610043K17Rik'>0610043K17Rik</a> +2610307P16Rik -0.91429583632135 -0.954931074728396 -1.03725537976782 0.317014922908806 0.457287012691463 -5.74201320442599 6 <a href='http://www.genecards.org/index.php?path=/Search/keyword/2610307P16Rik'>2610307P16Rik</a> +B630019K06Rik 0.719990612273558 -0.756810762138252 1.03218755693734 0.319301294119003 0.46000350579518 -5.72479023365126 7 <a href='http://www.genecards.org/index.php?path=/Search/keyword/B630019K06Rik'>B630019K06Rik</a> +Gm14872 0.835812662260224 -0.835052547360434 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href='http://www.genecards.org/index.php?path=/Search/keyword/Oaz1-ps'>Oaz1-ps</a> +Kcnq1ot1 0.910278085334024 -0.218382196489221 0.997758138243239 0.335150923261523 0.476223167423908 -5.74375068180754 16 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Kcnq1ot1'>Kcnq1ot1</a> +4921513I03Rik -0.898652409766853 -0.954931074728396 -0.996357559472656 0.335807392489445 0.476352069705573 -5.7819683962692 6 <a href='http://www.genecards.org/index.php?path=/Search/keyword/4921513I03Rik'>4921513I03Rik</a> +Snord111 0.487167361404432 2.40322325564047 0.995476712980872 0.336220726321058 0.476352069705573 -6.04721452535901 82 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord111'>Snord111</a> +Mir326 -0.382358415670825 3.27011368251419 -0.994342337417545 0.336753562180123 0.476352069705573 -6.21830968460093 144 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir326'>Mir326</a> +A330035P11Rik 0.965364268939122 -0.768738207773087 0.993167927399008 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href='http://www.genecards.org/index.php?path=/Search/keyword/Mir369'>Mir369</a> +Mir26a-2 0.485967334173185 2.96081541822386 0.904823661302764 0.380703847669755 0.519596997836352 -6.23863459210439 131 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir26a-2'>Mir26a-2</a> +Minos1 0.704827095217255 0.326231814341724 0.900400917247283 0.382972698552506 0.522069114753178 -5.81919593446542 22 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Minos1'>Minos1</a> +Deaf1 0.779036313891313 -0.299891783561682 0.896459320434846 0.385002448889921 0.524209778261814 -5.83491078724319 14 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Deaf1'>Deaf1</a> +Gm19466 -0.749840672361975 -1.04705177399917 -0.887587437647754 0.389597708777317 0.529834309552942 -5.89076869788414 5 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm19466'>Gm19466</a> +Gm2518 0.63646451042641 -0.558690449548107 0.883457449799982 0.391749438497377 0.532126320625604 -5.85297878336349 8 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm2518'>Gm2518</a> +Mir505 0.574628179268003 0.386589853479527 0.877080062325064 0.395087742631044 0.535616337424576 -5.8408806452811 16 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir505'>Mir505</a> +Gm13483 -0.650881842270608 -1.13917247326995 -0.876756483145742 0.395257630246707 0.535616337424576 -5.90961874985058 4 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm13483'>Gm13483</a> +A930016O22Rik -0.909159760956733 -0.165684653346019 -0.874712631220314 0.39633183750076 0.535965610314034 -5.83382312143566 20 <a href='http://www.genecards.org/index.php?path=/Search/keyword/A930016O22Rik'>A930016O22Rik</a> +4930526L06Rik -0.646483610508766 -1.13917247326995 -0.874478831554822 0.39645484233571 0.535965610314034 -5.91157337325639 4 <a href='http://www.genecards.org/index.php?path=/Search/keyword/4930526L06Rik'>4930526L06Rik</a> +1500011K16Rik 0.687958770706193 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href='http://www.genecards.org/index.php?path=/Search/keyword/Mir382'>Mir382</a> +Snord73a 0.572583034995795 1.81609219396321 0.851752202751694 0.408533400862583 0.548396012216715 -6.06031448455445 64 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord73a'>Snord73a</a> +AI450353 -0.739501717206301 -0.628239618113655 -0.84525729275282 0.412029489929552 0.551965918621367 -5.88226286676174 12 <a href='http://www.genecards.org/index.php?path=/Search/keyword/AI450353'>AI450353</a> +Rnf126 0.61640700457571 -0.941052160679803 0.844020033078334 0.412697708943189 0.551965918621367 -5.90363669815116 5 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rnf126'>Rnf126</a> +4930452A19Rik -0.567623714118899 -1.13917247326995 -0.842981854548559 0.41325895737657 0.551965918621367 -5.93813552591444 4 <a href='http://www.genecards.org/index.php?path=/Search/keyword/4930452A19Rik'>4930452A19Rik</a> +Mir20b -0.567623714118899 -1.13917247326995 -0.842981854548559 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href='http://www.genecards.org/index.php?path=/Search/keyword/B230208H11Rik'>B230208H11Rik</a> +Zfp207 0.813007063755825 -0.0836318824890616 0.828134659773233 0.421340237870797 0.556422698391875 -5.88719575711569 19 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Zfp207'>Zfp207</a> +Mir1945 0.597491165734377 -0.941052160679803 0.826047545337222 0.422484441705835 0.557288725995789 -5.91837835814761 5 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1945'>Mir1945</a> +Snora41 0.348564473053555 4.54185649419262 0.819592789265972 0.426035844548422 0.560279811338197 -6.58753509611365 394 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora41'>Snora41</a> +Oxsr1 0.724767749665156 0.244978069667359 0.819331396413772 0.426180068646681 0.560279811338197 -5.88476749078111 24 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Oxsr1'>Oxsr1</a> +D630024D03Rik 0.728476694326676 -1.31472125515486 0.818971143090679 0.426378890981613 0.560279811338197 -5.94729714256845 8 <a href='http://www.genecards.org/index.php?path=/Search/keyword/D630024D03Rik'>D630024D03Rik</a> +4933400L20Rik 0.515324865407562 -1.03317285995058 0.818083247017312 0.426869173233144 0.560279811338197 -5.9337772796173 4 <a href='http://www.genecards.org/index.php?path=/Search/keyword/4933400L20Rik'>4933400L20Rik</a> +Xist 0.723357937638788 -1.31472125515486 0.816666748076131 0.427652095638525 0.560279811338197 -5.94915534796961 8 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Xist'>Xist</a> +Dlg1 0.603909137429248 1.27329048309733 0.815752808761627 0.428157736836546 0.560279811338197 -5.99440605481118 45 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Dlg1'>Dlg1</a> +March2 0.877263658846623 0.62903919856468 0.815695775265458 0.428189303669507 0.560279811338197 -5.91500249911908 36 <a href='http://www.genecards.org/index.php?path=/Search/keyword/March2'>March2</a> +C230037L18Rik 0.602090880767705 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href='http://www.genecards.org/index.php?path=/Search/keyword/4930523C07Rik'>4930523C07Rik</a> +Mir374 0.289766495627774 4.44733832008286 0.806913394226144 0.433068070964141 0.562150931706581 -6.58616786299793 323 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir374'>Mir374</a> +Mir374c 0.289766495627774 4.44733832008286 0.806913394226144 0.433068070964141 0.562150931706581 -6.58616786299793 323 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir374c'>Mir374c</a> +Mir32 0.284410784956249 4.15923774757354 0.802255193307119 0.435670204852205 0.564332305440744 -6.54373122401893 274 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir32'>Mir32</a> +4930481A15Rik 0.749607671194882 -0.676617508502311 0.802134533319532 0.435737739783782 0.564332305440744 -5.92746695739246 12 <a href='http://www.genecards.org/index.php?path=/Search/keyword/4930481A15Rik'>4930481A15Rik</a> +Mir409 -0.359607138432163 2.88484526509054 -0.797779273016708 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href='http://www.genecards.org/index.php?path=/Search/keyword/Fut8'>Fut8</a> +Gm19522 -0.603683840589023 -0.590132795422603 -0.755842901826103 0.462139073141416 0.590653973169546 -5.94897829684297 8 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm19522'>Gm19522</a> +Mir874 0.295514313563059 4.89511091554138 0.755611590283585 0.462273442629627 0.590653973169546 -6.68933197812847 439 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir874'>Mir874</a> +5031425E22Rik 0.426232500568612 1.59819729877775 0.753049543565295 0.463763358388416 0.591894845549421 -6.09850103143821 41 <a href='http://www.genecards.org/index.php?path=/Search/keyword/5031425E22Rik'>5031425E22Rik</a> +2610203C22Rik 0.717338709985131 -0.478497195912167 0.74698345640789 0.46730279346032 0.595745795908632 -5.96274275496501 15 <a href='http://www.genecards.org/index.php?path=/Search/keyword/2610203C22Rik'>2610203C22Rik</a> +BC039771 0.591670069535226 -0.941052160679803 0.731476967640175 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href='http://www.genecards.org/index.php?path=/Search/keyword/2310040G24Rik'>2310040G24Rik</a> +Gm16973 0.520003601671916 -0.848931461409027 0.692816735376406 0.49963608955839 0.629232647004551 -6.01679548706659 8 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm16973'>Gm16973</a> +9430091E24Rik 0.632405272014803 1.08345345798668 0.690351426110223 0.501138492660048 0.630428908627469 -6.05646241852674 42 <a href='http://www.genecards.org/index.php?path=/Search/keyword/9430091E24Rik'>9430091E24Rik</a> +4930599N23Rik 0.731549498463023 -0.297616209139484 0.687698634645228 0.502758111464513 0.631137207128483 -5.99772425069657 22 <a href='http://www.genecards.org/index.php?path=/Search/keyword/4930599N23Rik'>4930599N23Rik</a> +Uqcc 0.60456771084976 0.00230964680615132 0.687617297753382 0.502807818825408 0.631137207128483 -5.98129860883947 18 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Uqcc'>Uqcc</a> +AF357425 -0.469274766892277 0.0356704882223264 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href='http://www.genecards.org/index.php?path=/Search/keyword/Adarb1'>Adarb1</a> +Gm2061 0.463825041047814 -1.39322515798149 0.636165822738289 0.534821761380555 0.656869353859217 -6.08891943947055 5 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm2061'>Gm2061</a> +G730013B05Rik -0.555071724179367 -0.202135098099839 -0.634045128592704 0.536165415013138 0.657811546806441 -6.00613726849612 14 <a href='http://www.genecards.org/index.php?path=/Search/keyword/G730013B05Rik'>G730013B05Rik</a> +Etohd2 0.50091939381951 -0.986373420602892 0.626287461136556 0.54109661778882 0.66314848646299 -6.06649536389095 6 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Etohd2'>Etohd2</a> +Fendrr 0.467194943660743 -1.03317285995058 0.625054288937282 0.541882799556935 0.663399435938265 -6.07231128308936 4 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Fendrr'>Fendrr</a> +Mir15a 0.206050012741693 7.92756591993174 0.624069296235348 0.542511213731924 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href='http://www.genecards.org/index.php?path=/Search/keyword/4921511C10Rik'>4921511C10Rik</a> +Rmrp 0.0655095097323271 7.670330005123 0.217766244863006 0.830719680954736 0.897584295976066 -7.21766694613943 3178 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rmrp'>Rmrp</a> +Ufd1l 0.195771351763775 -1.16497883295338 0.216430843996505 0.831740495954836 0.897584295976066 -6.26197687991093 7 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Ufd1l'>Ufd1l</a> +Snord70 0.10221174934082 2.60861620211668 0.21571068481477 0.832291135094371 0.897584295976066 -6.57150704500313 92 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord70'>Snord70</a> +Mrpl15 0.14880859252168 0.33979041413184 0.210945385298102 0.835937006061044 0.900604863671905 -6.19219624410467 16 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mrpl15'>Mrpl15</a> +Prmt1 0.168995528929063 -0.61462282166951 0.209987168816182 0.836670600781962 0.900604863671905 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href='http://www.genecards.org/index.php?path=/Search/keyword/Gm16039'>Gm16039</a> +1700007J10Rik -0.113205756535242 -0.788253108012747 -0.140564172695348 0.890195249337243 0.932061058543482 -6.24719705198026 7 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1700007J10Rik'>1700007J10Rik</a> +Nup88 -0.124975737193874 -0.239213430165402 -0.139113735537381 0.891320451556099 0.932061058543482 -6.20078805666017 15 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Nup88'>Nup88</a> +Mir1946b -0.11008548363065 0.157027195014887 -0.13736714896008 0.892675718878866 0.932061058543482 -6.19984394272254 15 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1946b'>Mir1946b</a> +Mirlet7g 0.0395844887395015 11.1837033910963 0.136145707336603 0.893623705801407 0.932061058543482 -7.47148737731621 38152 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mirlet7g'>Mirlet7g</a> +Gm10548 -0.0899680772947313 -0.34669122290937 -0.136099070118153 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href='http://www.genecards.org/index.php?path=/Search/keyword/C330013E15Rik'>C330013E15Rik</a> +5930430L01Rik 0.136225847581219 -0.214062543734675 0.119769549531324 0.906349281099135 0.941260828400483 -6.20916672317144 18 <a href='http://www.genecards.org/index.php?path=/Search/keyword/5930430L01Rik'>5930430L01Rik</a> +Mir496 0.0950067476259783 -0.0703291250970423 0.119430311967314 0.90661319054525 0.941260828400483 -6.20237905877004 13 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir496'>Mir496</a> +Mir669a-1 -0.0874831731028778 0.143148280966294 -0.118249227240961 0.907532102973484 0.941358299538859 -6.20192887859536 14 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir669a-1'>Mir669a-1</a> +Thap6 -0.0878168955885893 -0.558690449548107 -0.115414375847903 0.909738243408161 0.942789587401192 -6.2280381796423 8 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Thap6'>Thap6</a> +Chpt1 -0.127661446694368 0.920094239341047 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href='http://www.genecards.org/index.php?path=/Search/keyword/2610002J02Rik'>2610002J02Rik</a> +4921531C22Rik -0.0635851168193281 -0.941052160679803 -0.0822890634566592 0.93556934061789 0.959921241425124 -6.26957168238787 5 <a href='http://www.genecards.org/index.php?path=/Search/keyword/4921531C22Rik'>4921531C22Rik</a> +Srsf7 0.0705092857951172 -0.798864220211061 0.0812705943953252 0.936364891942299 0.959921241425124 -6.25432076732456 8 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Srsf7'>Srsf7</a> +1700020I14Rik 0.0749473297339094 0.656660491848086 0.0792648453094152 0.937931837290533 0.960664476075851 -6.23371457269478 32 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1700020I14Rik'>1700020I14Rik</a> +2210015D19Rik 0.0647102732837292 -1.23129317254072 0.0766096103443329 0.940006587546541 0.961787864403415 -6.29126291736405 5 <a href='http://www.genecards.org/index.php?path=/Search/keyword/2210015D19Rik'>2210015D19Rik</a> +4732416N19Rik 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href='http://www.genecards.org/index.php?path=/Search/keyword/Gm15441'>Gm15441</a> +Fam172a 0.0503754462959195 0.409161384184755 0.0596392630819191 0.953276904100091 0.970284520587158 -6.21618388102567 23 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Fam172a'>Fam172a</a> +Rbm18 -0.0538668143348915 -0.299891783561682 -0.0557642901053547 0.956309184092742 0.972503368137093 -6.21475268708383 12 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rbm18'>Rbm18</a> +Gm12191 -0.0354587706805078 -0.880373807283523 -0.0497068478436261 0.961050697355324 0.975480839012736 -6.26527518040501 6 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm12191'>Gm12191</a> +Rprl3 0.0408471478447264 -0.798864220211061 0.0488367850296659 0.961731876147215 0.975480839012736 -6.25649782741468 8 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rprl3'>Rprl3</a> +H19 -0.0415019911233814 -0.880373807283523 -0.0480992443304892 0.962309326654761 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-0.0253403588431765 -0.835052547360434 -0.031369255395874 0.975413152136616 0.984908324414052 -6.26109829686273 7 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Kcnk2'>Kcnk2</a> +A930011G23Rik -0.0241809579465951 -0.00965077170076215 -0.0291709235913898 0.977135635463562 0.985775207837245 -6.2074206456237 12 <a href='http://www.genecards.org/index.php?path=/Search/keyword/A930011G23Rik'>A930011G23Rik</a> +Mir3103 0.0180714470554271 -1.13917247326995 0.0259355368025229 0.979670906552206 0.987459809519494 -6.2920042186438 4 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3103'>Mir3103</a> +Snora75 -0.0172327656019052 -0.590132795422603 -0.021476287065286 0.983165572405378 0.989793060148976 -6.23767380603265 10 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora75'>Snora75</a> +4930414L22Rik -0.0152743869054217 -0.484133182103234 -0.0207679670021376 0.983720710086713 0.989793060148976 -6.22874423282067 8 <a href='http://www.genecards.org/index.php?path=/Search/keyword/4930414L22Rik'>4930414L22Rik</a> +Mipep 0.0164012673799433 -0.280376883322022 0.0179445082376201 0.985933647271923 0.991145631310365 -6.21618933242714 14 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mipep'>Mipep</a> +Ippk -0.0101933209515463 0.0857377294202925 -0.0128542290662295 0.989923536727642 0.99288598158411 -6.20831119150974 15 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Ippk'>Ippk</a> +Mir598 -0.00787301950188535 1.52736379718861 -0.0127956250729132 0.989969473858512 0.99288598158411 -6.3747989571524 44 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir598'>Mir598</a> +1500017E21Rik 0.0125149432592357 0.202348454937975 0.0124053255048405 0.990275413709656 0.99288598158411 -6.21004071500431 20 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1500017E21Rik'>1500017E21Rik</a> +Map1lc3a 0.00968300434227123 0.00717248334519302 0.0097742078067436 0.992337878036726 0.994080350166729 -6.20806203375241 21 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Map1lc3a'>Map1lc3a</a> +Trappc13 -0.00465914834988075 -0.880373807283523 -0.00622703745231414 0.995118499154886 0.995991410119056 -6.26653097741332 6 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Trappc13'>Trappc13</a> +Mir1966 -0.00246570556544304 -0.590132795422603 -0.00337044327478241 0.997357828291427 0.997357828291427 -6.23790561933129 8 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1966'>Mir1966</a>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gentestdata.sh Mon Dec 23 21:36:34 2013 -0500 @@ -0,0 +1,9 @@ +#!/bin/bash +# generate test data for rgGSEA +# ross lazarus June 2013 +# adjust gseajar_path ! +GSEAJAR_PATH=/home/rlazarus/galaxy-central/tool_dependency_dir/gsea_jar/2.0.12/fubar/rg_gsea_test/8e291f464aa0/jars/gsea2-2.0.12.jar +python ../rgGSEA.py --input_tab "gsea_test_DGE.xls" --adjpvalcol "5" --signcol "2" --idcol "1" --outhtml "gseatestout.html" --input_name "gsea_test" --setMax "500" --setMin "15" --nPerm "10" --plotTop "20" --gsea_jar "$GSEAJAR_PATH" --output_dir "gseatestout" --mode "Max_probe" +--title "GSEA test" --builtin_gmt "gseatestdata.gmt" + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_bams2mx.xls Mon Dec 23 21:36:34 2013 -0500 @@ -0,0 +1,3243 @@ +Contigname 11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam 11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam 11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam 11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam 11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam 11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam 11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam 11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam +0610005C13Rik 40 0 2 0 6 70 6 2 +0610007N19Rik 10 17 11 42 2 6 6 10 +0610008F07Rik 16 0 0 0 8 5 4 1 +0610009B14Rik 0 0 0 1 0 0 0 0 +0610009L18Rik 3 2 2 11 0 1 1 1 +0610012G03Rik 6 0 0 0 4 5 2 0 +0610031O16Rik 33 0 0 0 10 25 10 0 +0610038B21Rik 0 0 0 2 0 0 0 0 +0610038L08Rik 0 0 0 0 0 3 0 0 +0610039K10Rik 9 0 0 1 3 1 4 3 +0610040B10Rik 0 0 0 0 0 0 2 0 +0610040F04Rik 2 1 0 1 2 5 2 0 +0610043K17Rik 9 2 0 4 4 12 0 1 +1110002L01Rik 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Dec 23 21:36:34 2013 -0500 @@ -0,0 +1,50 @@ +<?xml version="1.0"?> +<tool_dependency> +<!-- + this will not compile for me - it thinks we have autoscaling on + - so we need libopenblas-base installed on all nodes...grrr + <package name="atlas" version="3.11.11"> + <repository name='package_atlas_3_11' owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + </package> + and we need this added to the set_environment section below too + <repository name="package_atlas_3_11" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/"> + <package name="atlas" version="3.11.11" /> + </repository> +--> + <package name="r3" version="3.0.1"> + <repository changeset_revision="6e89ec508745" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + </package> + <package name="ghostscript" version="9.07"> + <repository changeset_revision="7245d8573fca" name="package_ghostscript_9_07" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + </package> + <package name="graphicsmagick" version="1.3.18"> + <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + </package> + <package name="biocbasics" version="2.12"> + <install version="1.0"> + <actions> + <action type="set_environment_for_install"> + <repository changeset_revision="6e89ec508745" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> + <package name="r3" version="3.0.1" /> + </repository> + </action> + <action type="make_directory">$INSTALL_DIR</action> + <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" > $INSTALL_DIR/runme.R</action> + <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DESeq2')" >> $INSTALL_DIR/runme.R</action> + <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action> + <action type="shell_command">echo "biocLite(installme)" >> $INSTALL_DIR/runme.R</action> + <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T,repos='http://cran.us.r-project.org')" >> $INSTALL_DIR/runme.R</action> + <action type="shell_command">echo "quit(save='no')" >> $INSTALL_DIR/runme.R</action> + <action type="shell_command"> export PATH=$PATH && export R_HOME=$R_HOME && export R_LIBS=$R_LIBS && R CMD BATCH $INSTALL_DIR/runme.R </action> + </actions> + </install> + <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick + (replaces imagemagick) and ghostscript for compressing R's bloated pdfs + It's clunky but this is the most convenient way I could get anything installed into the package_r3 + Note we use cran at fred hutch since no fastest mirror thingy + copyright ross lazarus last updated december 2013 ross stop lazarus at gmail stop com + License to use this source (dependencies have their own obligations) + is made available to you under the terms of the LGPL + </readme> + </package> +</tool_dependency>