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1 <tool id="rgGSEAcolumns" name="Gene set enrichment" version="0.05">
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2 <description>using a generic tabular file</description>
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3 <requirements>
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4 <requirement type="package" version="2.0.12">gsea</requirement>
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5 <requirement type="set_environment">GSEAJAR_PATH</requirement>
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6 </requirements>
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7 <command interpreter="python">rgGSEA.py --input_tab "$input1" --adjpvalcol "$adjpvalcol" --signcol "$signcol"
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8 --idcol "$idcol" --outhtml "$html_file" --input_name "${input1.name}"
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9 --setMax "$setMax" --setMin "$setMin" --nPerm "$nPerm" --plotTop "$plotTop"
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10 --gsea_jar "\$GSEAJAR_PATH"
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11 --output_dir "$html_file.files_path" --mode "$mode" --title "$title"
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12 #if $makeTab.value=='Yes'
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13 --outtab_pos "$outtab_pos" --outtab_neg "$outtab_neg"
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14 #end if
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15 #if $gmtSource.refgmtSource == "indexed" or $gmtSource.refgmtSource == "both":
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16 --builtin_gmt "${gmtSource.builtinGMT.fields.path}"
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17 #end if
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18 #if $gmtSource.refgmtSource == "history" or $gmtSource.refgmtSource == "both":
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19 --history_gmt "${gmtSource.ownGMT}" --history_gmt_name "${gmtSource.ownGMT.name}"
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20 #end if
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21 #if $checkchip.convertchip=="yes"
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22 --chip "${checkchip.use_chip.fields.path}"
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23 #end if
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24 </command>
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25 <inputs>
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26 <param name="input1" type="data" format="tabular" label="Select a tab delimited file with a probe id, adjusted p value and a signed weight (eg t-test statistic) on each row"
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27 help=""/>
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28 <param name="adjpvalcol" label="Column containing a p value for the DEG statistical test"
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29 help = "Use RAW p-values - not FDR adjusted as these have a non GSEA friendly non-uniform distribution"
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30 type="data_column" data_ref="input1" numerical="True"
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31 multiple="false" use_header_names="true" size="5">
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32 <validator type="no_options" message="Please select a p value column."/>
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33 </param>
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34 <param name="signcol" label="Column containing the DE sign - eg log fold change so positive/negative values = upregulated/downregulated in treatment"
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35 type="data_column" data_ref="input1" numerical="True"
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36 multiple="false" use_header_names="true" size="5">
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37 <validator type="no_options" message="Please select a sign column."/>
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38 </param>
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39 <param name="idcol" label="Column containing a gene id (refseq, symbol or Entrez"
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40 type="data_column" data_ref="input1" numerical="False"
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41 multiple="false" use_header_names="true" size="5">
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42 <validator type="no_options" message="Please select an id column."/>
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43 </param>
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44
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45 <param name="title" type="text" value="GSEA" size="80" label="Title for job outputs" help="Supply a meaningful name here to remind you what the outputs contain"/>
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46 <param name="setMin" type="integer" label="Minimum gene set size to prune (default=15)" size="5" value="15"/>
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47 <param name="setMax" type="integer" label="Maximum gene set size to prune (default=500)" size="5" value="500"/>
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48 <param name="nPerm" type="integer" label="Number of permutations (default=1000)" size="7" value="1000"/>
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49 <param name="plotTop" type="integer" label="Number of top gene sets to plot and present in detailed reports(default=20)" size="10" value="20"/>
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50 <param name="mode" type="select" label="Mode for dealing with duplicated gene ids" >
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51 <option value="Max_probe" selected="true">Use the most extreme value</option>
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52 <option value="Median_of_probes">Use the median of all supplied values</option>
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53 </param>
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54 <param name="makeTab" type="select" label="Create a tabular report containing ALL gene sets for downstream analysis" >
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55 <option value="Yes">Yes</option>
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56 <option value="No" selected="true">No</option>
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57 </param>
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58 <conditional name="checkchip" >
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59 <param name="convertchip" type="select" label="Translate the rank file IDs (first column) using a GSEA 'chip' lookup table">
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60 <option value="yes">Use a GSEA 'chip' file</option>
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61 <option value="no" selected="true">IDs are already gene symbols - no translation needed </option>
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62 </param>
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63 <when value="no">
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64 </when>
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65 <when value="yes">
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66 <param name="use_chip" type="select" label="Select a GSEA 'chip' for the probe ids or symbols in the ranks file">
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67 <options from_data_table="gseaChip_3.1">
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68 <filter type="sort_by" column="2" />
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69 <validator type="no_options" message="No chip tables are available - please see the Galaxy GSEA tool documentation for instructions on installing them" />
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70 </options>
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71 </param>
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72 </when>
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73 </conditional>
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74 <conditional name="gmtSource">
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75 <param name="refgmtSource" type="select" label="Use a gene set (.gmt) from your history or use a built-in (MSigDB etc) gene set">
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76 <option value="indexed" selected="true">Use a built-in gene set</option>
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77 <option value="history">Use a gene set from my history</option>
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78 <option value="both">Add a gene set from my history to a built in gene set</option>
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79 </param>
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80 <when value="indexed">
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81 <param name="builtinGMT" type="select" label="Select a gene set matrix (.gmt) file to use for the analysis">
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82 <options from_data_table="gseaGMT_3.1">
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83 <filter type="sort_by" column="2" />
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84 <validator type="no_options" message="No GMT v3.1 files are available - please install them"/>
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85 </options>
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86 </param>
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87 </when>
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88 <when value="history">
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89 <param name="ownGMT" type="data" format="gmt" label="Select a Gene Set from your history" />
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90 </when>
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91 <when value="both">
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92 <param name="ownGMT" type="data" format="gmt" label="Select a Gene Set from your history" />
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93 <param name="builtinGMT" type="select" label="Select a gene set matrix (.gmt) file to use for the analysis">
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94 <options from_data_table="gseaGMT_3.1">
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95 <filter type="sort_by" column="2" />
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96 <validator type="no_options" message="No GMT v3.1 files are available - please install them"/>
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97 </options>
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98 </param>
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99 </when>
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100 </conditional>
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101 </inputs>
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102 <outputs>
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103 <data format="html" name="html_file" label="${title}.html"/>
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104 <data format="tabular" name="outtab_pos" label="${title}_pos_allsets.xls">
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105 <filter>makeTab=="Yes"</filter>
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106 </data>
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107 <data format="tabular" name="outtab_neg" label="${title}_neg_allsets.xls">
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108 <filter>makeTab=="Yes"</filter>
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109 </data>
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110
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111 </outputs>
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112 <help>
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113 **What it does**
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114
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115 Performs Gene set enrichment analysis using GSEA_ from the Broad as described in 2005Paper_ and v3.1 of msigdb
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116
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117 Refer to http://www.pnas.org/cgi/content/abstract/0506580102v1 for details of the method.
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118
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119 **Input**
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120
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121 A tabular file with a header row and some columns containing probe ids or gene names; a p value or t-test statistic reflecting the
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122 strength and a signed quantity such as log fold change or a t-test statistic reflecting the direction of differential gene expression from edgeR for counts
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123 or some other valid analysis.
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124 Probe names can be translated using the chip file option (see below)
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125 A filter has been added to remove NA and null id rows as these can't be used. A summary will appear in stdout in the page linked from the "i" (info) button for the output
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126
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127 **Gene sets**
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128
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129 If you have your own gene sets as .gmt files (see GUIDE_ for details of format) upload them in your history and use them by nominating a history sourced gmt.
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130
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131 Alternatively, use one of the built in MSigDB_ (molecular signatures database) sets.
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132 There may be additional locally provided sets such as starBase
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133
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134 Optionally, a local gmt can be merged with a built in one if you want to see how they perform competitively
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135
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136 Select the most appropriate subset of MSigDB gene sets or use all by choosing msigdb.v3.0.symbols.
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137 A non-cancer subset called c2_c3_c5_all.v3.0.symbols is recommended if you are working with non-cancer biology.
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138
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139
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140 **Chip**
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141
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142 If your input file contains HUGO gene symbols (TEK, SLC38A1...etc) then you do not need to specify a 'chip'.
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143
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144 GSEA software allows you to specify a translation table from common microarray probe IDs to gene symbols - select the option to use a chip file and choose the one that matches your probe id's
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145 Failure to match the translation correctly will generally result in failure of the job since none of your input data will be translated properly.
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146
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147 **Output**
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148
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149 A report as html - see the GUIDE_ for a guide on interpretation
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150
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151
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152 **Attribution**
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153
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154 This Galaxy tool wrapper was written by Ross Lazarus.
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155 It executes the GSEA_ java application available using MSigDB and Chip files obtained from the GSEA_ web site
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156
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157
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158 **Chip ID samples**
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159
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160 You may be able to look for probe ids in similar form to the ones you have in the list below to find the correct GSEA 'chip' file if you do not have HUGO gene symbols
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161
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162 ::
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163
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164 AG.chip
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165 Probe Set ID Gene Symbol Gene Title
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166 11986_at --- calcium-dependent lipid-binding protein, putative
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167 11987_at --- zinc finger (C3HC4-type RING finger) family protein
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168 11988_at --- WD-40 repeat family protein
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169
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170 Agilent_Human1A.chip
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171 Probe Set ID Gene Symbol Gene Title
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172 A_23_P100001 LOC400451 hypothetical gene supported by AK075564; BC060873
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173 A_23_P100011 AP3S2 adaptor-related protein complex 3, sigma 2 subunit
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174 A_23_P10002 CEP63 centrosome protein Cep63
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175
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176 Agilent_Human1Av2.chip
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177 Probe Set ID Gene Symbol Gene Title
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178 A_23_P100001 LOC400451 hypothetical gene supported by AK075564; BC060873
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179 A_23_P100011 AP3S2 adaptor-related protein complex 3, sigma 2 subunit
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180 A_23_P10002 CEP63 centrosome protein Cep63
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181
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182 Agilent_Human1B.chip
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183 Probe Set ID Gene Symbol Gene Title
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184 A_32_P10002 TUBA2 tubulin, alpha 2
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185 A_32_P100076 RPL19 ribosomal protein L19
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186 A_32_P100100 THOC3 THO complex 3
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187
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188 Agilent_Human1_cDNA.chip
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189 Probe Set ID Gene Symbol Gene Title
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190 1 RNASEH2A ribonuclease H2, large subunit
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191 10 SF3B1 splicing factor 3b, subunit 1, 155kDa
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192 100 S100A16 S100 calcium binding protein A16
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193
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194 Agilent_HumanGenome.chip
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195 Probe Set ID Gene Symbol Gene Title
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196 A_23_P100001 LOC400451 hypothetical gene supported by AK075564; BC060873
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197 A_23_P100011 NULL NULL
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198 A_23_P100022 SV2B synaptic vesicle glycoprotein 2B
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199
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200 Agilent_Mouse_cDNA.chip
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201 Probe Set ID Gene Symbol Gene Title
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202 1000982 SLC6A9 solute carrier family 6 (neurotransmitter transporter, glycine), member 9
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203 1001007 IGF1 insulin-like growth factor 1
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204 1001011 FCNA ficolin A
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205
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206 Agilent_MouseDev.chip
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207 Probe Set ID Gene Symbol Gene Title
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208 A_65_P00523 NULL NULL
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209 A_65_P00524 NULL NULL
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210 A_65_P00525 SFTPD surfactant associated protein D
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211
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212 Agilent_MouseGenome.chip
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213 Probe Set ID Gene Symbol Gene Title
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214 A_51_P100021 NULL NULL
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215 A_51_P100034 2310075G12RIK RIKEN cDNA 2310075G12 gene
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216 A_51_P100052 SLITRK2 SLIT and NTRK-like family, member 2
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217
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218 Agilent_MouseOligo.chip
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219 Probe Set ID Gene Symbol Gene Title
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220 A_51_P100021 NULL NULL
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221 A_51_P100034 2310075G12RIK RIKEN cDNA 2310075G12 gene
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222 A_51_P100052 SLITRK2 SLIT and NTRK-like family, member 2
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223
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224 Agilent_RatGenome_G4131A.chip
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225 Probe Set ID Gene Symbol Gene Title
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226 A_42_P453055 LU Lutheran blood group (Auberger b antigen included)
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227 A_42_P453737 NULL NULL
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228 A_42_P453894 RGD1306682_PREDICTED similar to RIKEN cDNA 1810046J19 (predicted)
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229
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230 Agilent_RatOligo.chip
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231 Probe Set ID Gene Symbol Gene Title
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232 A_42_P453131 CNTN1 contactin 1
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233 A_42_P453151 TTC8_PREDICTED tetratricopeptide repeat domain 8 (predicted)
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234 A_42_P453162 NULL NULL
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235
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236 APPLERA_ABI1700.chip
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237 Probe Set ID Gene Symbol Gene Title
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238 100002 NULL NULL
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239 100003 NULL NULL
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240 100027 ZNF192 zinc finger protein 192
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241
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242 ATH1_121501.chip
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243 Probe Set ID Gene Symbol Gene Title
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244 244901_at --- ---
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245 244902_at --- ---
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246 244903_at --- ---
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247
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248 AtlasMouse1.2.chip
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249 Probe Set ID Gene Symbol Gene Title
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250 MA099 HTR1A 5-hydroxytryptamine (serotonin) receptor 1A
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251 MA015 JARID2 jumonji, AT rich interactive domain 2
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252 M443 CDKN2C cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)
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253
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254 AtlasRat1.2.chip
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255 Probe Set ID Gene Symbol Gene Title
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256 R484 TPP2 tripeptidylpeptidase II
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257 RG348 MOS v-mos moloney murine sarcoma viral oncogene homolog
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258 RG119 KCNJ1 potassium inwardly-rectifying channel, subfamily J, member 1
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259
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260 Bovine.chip
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261 Probe Set ID Gene Symbol Gene Title
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262 AFFX-BioB-3_at --- ---
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263 AFFX-BioB-5_at --- ---
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264 AFFX-BioB-M_at --- ---
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265
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266 Caltech16KMouse.chip
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267 Probe Set ID Gene Symbol Gene Title
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268 6712 CCL6 chemokine (C-C motif) ligand 6
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269 8563 ACTL7B actin-like 7b
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270 8434 1700049M11RIK RIKEN cDNA 1700049M11 gene
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271
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272 Caltech16KOligoMouse.chip
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273 Probe Set ID Gene Symbol Gene Title
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274 6712 GCA grancalcin, EF-hand calcium binding protein
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275 8563 MARVELD2 MARVEL (membrane-associating) domain containing 2
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276 8434 BC048825 NULL
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277
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278 Canine_2.chip
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279 Probe Set ID Gene Symbol Gene Title
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280 AFFX-BioB-3_at --- ---
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281 AFFX-BioB-5_at --- ---
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282 AFFX-BioB-M_at --- ---
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283
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284 Clontech_Atlas_13K.chip
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285 Probe Set ID Gene Symbol Gene Title
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286 1-A01 NULL NULL
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287 1-A02 A2M alpha-2-macroglobulin
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288 1-A03 AADAC arylacetamide deacetylase (esterase)
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289
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290 Clontech_BD_Atlas.chip
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291 Probe Set ID Gene Symbol Gene Title
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292 A01a PCP4 Purkinje cell protein 4
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293 A01b NULL NULL
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294 A01c PMP22 peripheral myelin protein
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295
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296 CNMCMuscleChip.chip
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297 Probe Set ID Gene Symbol Gene Title
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298 HSPD4570_at MBP myelin basic protein
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299 HSPD7328_at MAPK12 mitogen-activated protein kinase 12
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300 HSPD17028_i_at DIA1 diaphorase (NADH) (cytochrome b-5 reductase)
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301
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302 CodeLink_Human_Whole_Genome.chip
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303 Probe Set ID Gene Symbol Gene Title
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304 GE469530 NULL NULL
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305 GE469548 TMEM1 transmembrane protein 1
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306 GE469549 NULL NULL
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307
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308 CodeLink_UniSet_Human_20K_I_Bioarray.chip
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309 Probe Set ID Gene Symbol Gene Title
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310 000106CB1_PROBE1 NDUFA4 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4, 9kDa
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311 000136CB1_PROBE1 MRPS33 mitochondrial ribosomal protein S33
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312 000278CB1_PROBE1 FDFT1 farnesyl-diphosphate farnesyltransferase 1
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313
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314 CodeLink_UniSet_Human_I_Bioarray.chip
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315 Probe Set ID Gene Symbol Gene Title
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316 AA001334_PROBE1 ZHX2 zinc fingers and homeoboxes 2
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317 AA002191_PROBE1 PITPNA phosphatidylinositol transfer protein, alpha
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318 AA004381_PROBE1 NULL NULL
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319
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320 CodeLink_UniSet_Human_II_Bioarray.chip
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321 Probe Set ID Gene Symbol Gene Title
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322 000106CB1_PROBE1 NDUFA4 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4, 9kDa
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323 000136CB1_PROBE1 MRPS33 mitochondrial ribosomal protein S33
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324 000278CB1_PROBE1 FDFT1 farnesyl-diphosphate farnesyltransferase 1
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325
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326 CodeLink_UniSet_Rat_I_Bioarray.chip
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327 Probe Set ID Gene Symbol Gene Title
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328 AA799301_PROBE1 NULL NULL
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329 AA799313_PROBE1 RGD:1303279 sialyltransferase 10 (alpha-2,3-sialyltransferase VI)
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330 AA799329_PROBE1 NULL NULL
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331
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332 DrosGenome1.chip
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333 Probe Set ID Gene Symbol Gene Title
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334 141200_at CG9418 CG9418
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335 141201_at CG17840 CG17840
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336 141202_at QKR58E-3 quaking related 58E-3
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337
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338 Drosophila_2.chip
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339 Probe Set ID Gene Symbol Gene Title
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340 1616608_a_at GPDH Glycerol 3 phosphate dehydrogenase
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341 1622892_s_at CG33057 /// MKG-P CG33057 /// monkey king protein
|
|
|
342 1622893_at IM3 /// RPS10B Immune induced molecule 3 /// Ribosomal protein S10b
|
|
|
343
|
|
|
344 G4110A.chip
|
|
|
345 Probe Set ID Gene Symbol Gene Title
|
|
|
346 A_23_P7033 MAGEF1 melanoma antigen, family F, 1
|
|
|
347 A_23_P170713 A_23_P170713 ***description missing***
|
|
|
348 A_23_P107801 FLJ21742 hypothetical protein FLJ21742
|
|
|
349
|
|
|
350 G4110Av2.chip
|
|
|
351 Probe Set ID Gene Symbol Gene Title
|
|
|
352 A_23_P7033 MAGEF1 melanoma antigen, family F, 1
|
|
|
353 A_23_P170713 A_23_P170713 No description available
|
|
|
354 A_23_P107801 FLJ21742 hypothetical protein FLJ21742
|
|
|
355
|
|
|
356 GENE_SYMBOL.chip
|
|
|
357 Probe Set ID Gene Symbol Gene Title Aliases
|
|
|
358 A1BG A1BG alpha-1-B glycoprotein GABDKFZP686F0970ABGHYST2477A1B
|
|
|
359 A2M A2M alpha-2-macroglobulin DKFZP779B086S863-7ALPHA 2MFWP007CPAMD5
|
|
|
360 A2ML1 A2ML1 alpha-2-macroglobulin-like 1 FLJ39129DKFZP686O1010FLJ41598DKFZP686G1812FLJ25179CPAMD9DKFZP686D2011FLJ16045FLJ41607DKFZP686C1729FLJ41597DKFZP686L1821
|
|
|
361
|
|
|
362 GenosysCytokineV2.chip
|
|
|
363 Probe Set ID Gene Symbol Gene Title
|
|
|
364 M05.2 GDF11 growth differentiation factor 11
|
|
|
365 M22.2 AE000170 No description available
|
|
|
366 E06.3 IL5 interleukin 5 (colony-stimulating factor, eosinophil)
|
|
|
367
|
|
|
368 HC_G110.chip
|
|
|
369 Probe Set ID Gene Symbol Gene Title
|
|
|
370 1000_at MAPK3 mitogen-activated protein kinase 3
|
|
|
371 1001_at TIE1 tyrosine kinase with immunoglobulin-like and EGF-like domains 1
|
|
|
372 1002_f_at CYP2C19 cytochrome P450, family 2, subfamily C, polypeptide 19
|
|
|
373
|
|
|
374 HG_Focus.chip
|
|
|
375 Probe Set ID Gene Symbol Gene Title
|
|
|
376 1007_s_at DDR1 discoidin domain receptor family, member 1
|
|
|
377 1053_at RFC2 replication factor C (activator 1) 2, 40kDa
|
|
|
378 117_at HSPA6 /// LOC652878 heat shock 70kDa protein 6 (HSP70B') /// similar to heat shock 70kDa protein 6 (HSP70B)
|
|
|
379
|
|
|
380 HG_U133A_2.chip
|
|
|
381 Probe Set ID Gene Symbol Gene Title
|
|
|
382 1007_s_at DDR1 discoidin domain receptor family, member 1
|
|
|
383 1053_at RFC2 replication factor C (activator 1) 2, 40kDa
|
|
|
384 117_at HSPA6 /// LOC652878 heat shock 70kDa protein 6 (HSP70B') /// similar to heat shock 70kDa protein 6 (HSP70B)
|
|
|
385
|
|
|
386 HG_U133AAofAv2.chip
|
|
|
387 Probe Set ID Gene Symbol Gene Title
|
|
|
388 1007_s_at DDR1 discoidin domain receptor family, member 1
|
|
|
389 1053_at RFC2 replication factor C (activator 1) 2, 40kDa
|
|
|
390 117_at HSPA6 /// LOC652878 heat shock 70kDa protein 6 (HSP70B') /// similar to heat shock 70kDa protein 6 (HSP70B)
|
|
|
391
|
|
|
392 HG_U133A.chip
|
|
|
393 Probe Set ID Gene Symbol Gene Title
|
|
|
394 1007_s_at DDR1 discoidin domain receptor family, member 1
|
|
|
395 1053_at RFC2 replication factor C (activator 1) 2, 40kDa
|
|
|
396 117_at HSPA6 /// LOC652878 heat shock 70kDa protein 6 (HSP70B') /// similar to heat shock 70kDa protein 6 (HSP70B)
|
|
|
397
|
|
|
398 HG_U133B.chip
|
|
|
399 Probe Set ID Gene Symbol Gene Title
|
|
|
400 200000_s_at PRPF8 PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae) /// PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)
|
|
|
401 200001_at CAPNS1 calpain, small subunit 1 /// calpain, small subunit 1
|
|
|
402 200002_at RPL35 ribosomal protein L35 /// ribosomal protein L35
|
|
|
403
|
|
|
404 HG_U133_Plus_2.chip
|
|
|
405 Probe Set ID Gene Symbol Gene Title
|
|
|
406 1007_s_at DDR1 discoidin domain receptor family, member 1
|
|
|
407 1053_at RFC2 replication factor C (activator 1) 2, 40kDa
|
|
|
408 117_at HSPA6 /// LOC652878 heat shock 70kDa protein 6 (HSP70B') /// similar to heat shock 70kDa protein 6 (HSP70B)
|
|
|
409
|
|
|
410 HG_U95Av2.chip
|
|
|
411 Probe Set ID Gene Symbol Gene Title
|
|
|
412 1000_at MAPK3 mitogen-activated protein kinase 3
|
|
|
413 1001_at TIE1 tyrosine kinase with immunoglobulin-like and EGF-like domains 1
|
|
|
414 1002_f_at CYP2C19 cytochrome P450, family 2, subfamily C, polypeptide 19
|
|
|
415
|
|
|
416 HG_U95B.chip
|
|
|
417 Probe Set ID Gene Symbol Gene Title
|
|
|
418 41880_at --- Transcribed locus
|
|
|
419 41881_at FLJ40142 FLJ40142 protein
|
|
|
420 41882_at FBXO42 F-box protein 42
|
|
|
421
|
|
|
422 HG_U95C.chip
|
|
|
423 Probe Set ID Gene Symbol Gene Title
|
|
|
424 48609_r_at KIAA1333 KIAA1333
|
|
|
425 48610_at C20ORF102 chromosome 20 open reading frame 102
|
|
|
426 48612_at N4BP1 /// LOC653213 Nedd4 binding protein 1 /// similar to Nedd4 binding protein 1
|
|
|
427
|
|
|
428 HG_U95D.chip
|
|
|
429 Probe Set ID Gene Symbol Gene Title
|
|
|
430 67020_at --- Transcribed locus
|
|
|
431 67021_at FAM44B Family with sequence similarity 44, member B
|
|
|
432 67023_at --- Transcribed locus
|
|
|
433
|
|
|
434 HG_U95E.chip
|
|
|
435 Probe Set ID Gene Symbol Gene Title
|
|
|
436 67022_at PIP5K2B Phosphatidylinositol-4-phosphate 5-kinase, type II, beta
|
|
|
437 67024_at CASD1 CAS1 domain containing 1
|
|
|
438 67026_at NFASC neurofascin homolog (chicken)
|
|
|
439
|
|
|
440 HPCGGCompugenAnnotations.chip
|
|
|
441 Probe Set ID Gene Symbol Gene Title
|
|
|
442 MGI:1913066 SH3MD2 Sh3md2, SH3 multiple domains 2
|
|
|
443 MGI:1913099 5430413I02RIK 5430413I02Rik, RIKEN cDNA 5430413I02 gene
|
|
|
444 MGI:98848 TSHB Tshb, thyroid stimulating hormone, beta subunit
|
|
|
445
|
|
|
446 HT_HG_U133A.chip
|
|
|
447 Probe Set ID Gene Symbol Gene Title
|
|
|
448 1007_s_at DDR1 discoidin domain receptor family, member 1
|
|
|
449 1053_at RFC2 replication factor C (activator 1) 2, 40kDa
|
|
|
450 117_at HSPA6 /// LOC652878 heat shock 70kDa protein 6 (HSP70B') /// similar to heat shock 70kDa protein 6 (HSP70B)
|
|
|
451
|
|
|
452 Hu35KsubA.chip
|
|
|
453 Probe Set ID Gene Symbol Gene Title
|
|
|
454 AA000993_at PRDM8 PR domain containing 8
|
|
|
455 AA001296_s_at PHF23 PHD finger protein 23
|
|
|
456 AA002245_at ZC3H11A zinc finger CCCH-type containing 11A
|
|
|
457
|
|
|
458 Hu35KsubB.chip
|
|
|
459 Probe Set ID Gene Symbol Gene Title
|
|
|
460 AFFX-BioB-3_at --- ---
|
|
|
461 AFFX-BioB-3_st --- ---
|
|
|
462 AFFX-BioB-5_at --- ---
|
|
|
463
|
|
|
464 Hu35KsubC.chip
|
|
|
465 Probe Set ID Gene Symbol Gene Title
|
|
|
466 AFFX-BioB-3_at --- ---
|
|
|
467 AFFX-BioB-3_st --- ---
|
|
|
468 AFFX-BioB-5_at --- ---
|
|
|
469
|
|
|
470 Hu35KsubD.chip
|
|
|
471 Probe Set ID Gene Symbol Gene Title
|
|
|
472 AFFX-BioB-3_at --- ---
|
|
|
473 AFFX-BioB-3_st --- ---
|
|
|
474 AFFX-BioB-5_at --- ---
|
|
|
475
|
|
|
476 Hu6800.chip
|
|
|
477 Probe Set ID Gene Symbol Gene Title
|
|
|
478 A28102_at GABRA3 gamma-aminobutyric acid (GABA) A receptor, alpha 3
|
|
|
479 AB000114_at OMD osteomodulin
|
|
|
480 AB000115_at IFI44L interferon-induced protein 44-like
|
|
|
481
|
|
|
482 Illumina_Human.chip
|
|
|
483 Probe Set ID Gene Symbol Gene Title
|
|
|
484 1-A-1 BCAP31 B-cell receptor-associated protein 31
|
|
|
485 1-A-10 NSFL1C NSFL1 (p97) cofactor (p47)
|
|
|
486 1-A-11 C20ORF24 chromosome 20 open reading frame 24
|
|
|
487
|
|
|
488 ilmn_HumanHT_12_V4_0_R1_15002873_B.chip
|
|
|
489 Probe Set ID Gene Symbol Gene Title Entrez Gene ID
|
|
|
490 ILMN_1725881 LOC23117 PREDICTED: Homo sapiens KIAA0220-like protein, transcript variant 11 (LOC23117), mRNA. 23117
|
|
|
491 ILMN_1910180 Homo sapiens cDNA: FLJ21027 fis, clone CAE07110 -999
|
|
|
492 ILMN_1804174 FCGR2B PREDICTED: Homo sapiens Fc fragment of IgG, low affinity IIb, receptor (CD32) (FCGR2B), mRNA. 2213
|
|
|
493
|
|
|
494 ilmn_MouseRef_8_V2_0_R3_11278551_A.chip
|
|
|
495 Probe Set ID Gene Symbol Gene Title Entrez Gene ID
|
|
|
496 ILMN_2607609 YIF1B Mus musculus Yip1 interacting factor homolog B (S. cerevisiae) (Yif1b), mRNA. 77254
|
|
|
497 ILMN_1238674 2700007P21RIK Mus musculus RIKEN cDNA 2700007P21 gene (2700007P21Rik), transcript variant 2, mRNA. 212772
|
|
|
498 ILMN_3062534 2700007P21RIK Mus musculus RIKEN cDNA 2700007P21 gene (2700007P21Rik), transcript variant 2, mRNA. 212772
|
|
|
499
|
|
|
500 ilmn_MouseWG_6_V2_0_R3_11278593_A.chip
|
|
|
501 Probe Set ID Gene Symbol Gene Title Entrez Gene ID
|
|
|
502 ILMN_1243094 THRSP NULL -999
|
|
|
503 ILMN_1238674 2700007P21RIK Mus musculus RIKEN cDNA 2700007P21 gene (2700007P21Rik), transcript variant 2, mRNA. 212772
|
|
|
504 ILMN_2454720 2700007P21RIK Mus musculus RIKEN cDNA 2700007P21 gene (2700007P21Rik), transcript variant 2, mRNA. 212772
|
|
|
505
|
|
|
506 labonweb_human.chip
|
|
|
507 Probe Set ID Gene Symbol Gene Title
|
|
|
508 1-A1 GAPD glyceraldehyde-3-phosphate dehydrogenase
|
|
|
509 1-A10 BMP5 bone morphogenetic protein 5
|
|
|
510 1-A11 C9ORF78 chromosome 9 open reading frame 78
|
|
|
511
|
|
|
512 lymphochip.chip
|
|
|
513 Probe Set ID Gene Symbol Gene Title
|
|
|
514 1317148 TNF tumor necrosis factor (TNF superfamily, member 2)
|
|
|
515 814251 SLAMF1 signaling lymphocytic activation molecule family member 1
|
|
|
516 712899___1 AA282233 zt12d02.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone
|
|
|
517
|
|
|
518 MG_U74Av2.chip
|
|
|
519 Probe Set ID Gene Symbol Gene Title
|
|
|
520 100001_at CD3G CD3 antigen, gamma polypeptide
|
|
|
521 100002_at ITIH3 inter-alpha trypsin inhibitor, heavy chain 3
|
|
|
522 100003_at RYR1 ryanodine receptor 1, skeletal muscle
|
|
|
523
|
|
|
524 MG_U74Bv2.chip
|
|
|
525 Probe Set ID Gene Symbol Gene Title
|
|
|
526 104769_at LIMA1 LIM domain and actin binding 1
|
|
|
527 104770_at --- 16 days neonate heart cDNA, RIKEN full-length enriched library, clone:D830033B01 product:unclassifiable, full insert sequence
|
|
|
528 104771_at RAC2 RAS-related C3 botulinum substrate 2
|
|
|
529
|
|
|
530 MG_U74Cv2.chip
|
|
|
531 Probe Set ID Gene Symbol Gene Title
|
|
|
532 128520_at CCDC97 coiled-coil domain containing 97
|
|
|
533 128523_at A730063M14RIK RIKEN cDNA A730063M14 gene
|
|
|
534 128529_at A930009G19RIK RIKEN cDNA A930009G19 gene
|
|
|
535
|
|
|
536 MOE430A.chip
|
|
|
537 Probe Set ID Gene Symbol Gene Title
|
|
|
538 1415670_at COPG coatomer protein complex, subunit gamma
|
|
|
539 1415671_at ATP6V0D1 ATPase, H+ transporting, lysosomal V0 subunit D1
|
|
|
540 1415672_at GOLGA7 golgi autoantigen, golgin subfamily a, 7
|
|
|
541
|
|
|
542 MOE430B.chip
|
|
|
543 Probe Set ID Gene Symbol Gene Title
|
|
|
544 1415670_at COPG coatomer protein complex, subunit gamma
|
|
|
545 1415671_at ATP6V0D1 ATPase, H+ transporting, lysosomal V0 subunit D1
|
|
|
546 1415672_at GOLGA7 golgi autoantigen, golgin subfamily a, 7
|
|
|
547
|
|
|
548 Mouse430_2.chip
|
|
|
549 Probe Set ID Gene Symbol Gene Title
|
|
|
550 1415670_at COPG coatomer protein complex, subunit gamma
|
|
|
551 1415671_at ATP6V0D1 ATPase, H+ transporting, lysosomal V0 subunit D1
|
|
|
552 1415672_at GOLGA7 golgi autoantigen, golgin subfamily a, 7
|
|
|
553
|
|
|
554 Mouse430A_2.chip
|
|
|
555 Probe Set ID Gene Symbol Gene Title
|
|
|
556 1415670_at COPG coatomer protein complex, subunit gamma
|
|
|
557 1415671_at ATP6V0D1 ATPase, H+ transporting, lysosomal V0 subunit D1
|
|
|
558 1415672_at GOLGA7 golgi autoantigen, golgin subfamily a, 7
|
|
|
559
|
|
|
560 Mu11KsubA.chip
|
|
|
561 Probe Set ID Gene Symbol Gene Title
|
|
|
562 aa000148_s_at NIP7 nuclear import 7 homolog (S. cerevisiae)
|
|
|
563 AA000151_at 1200011I18RIK RIKEN cDNA 1200011I18 gene
|
|
|
564 aa000380_s_at TARDBP TAR DNA binding protein
|
|
|
565
|
|
|
566 Mu11KsubB.chip
|
|
|
567 Probe Set ID Gene Symbol Gene Title
|
|
|
568 AFFX-18SRNAMur/X00686_3_at --- ---
|
|
|
569 AFFX-18SRNAMur/X00686_5_at --- ---
|
|
|
570 AFFX-18SRNAMur/X00686_M_at --- ---
|
|
|
571
|
|
|
572 Mu19KsubA.chip
|
|
|
573 Probe Set ID Gene Symbol Gene Title
|
|
|
574 AFFX-18SRNAMur/X00686_3_at --- ---
|
|
|
575 AFFX-18SRNAMur/X00686_5_at --- ---
|
|
|
576 AFFX-18SRNAMur/X00686_M_at --- ---
|
|
|
577
|
|
|
578 Mu19KsubB.chip
|
|
|
579 Probe Set ID Gene Symbol Gene Title
|
|
|
580 AFFX-18SRNAMur/X00686_3_at --- ---
|
|
|
581 AFFX-18SRNAMur/X00686_5_at --- ---
|
|
|
582 AFFX-18SRNAMur/X00686_M_at --- ---
|
|
|
583
|
|
|
584 Mu19KsubC.chip
|
|
|
585 Probe Set ID Gene Symbol Gene Title
|
|
|
586 AFFX-18SRNAMur/X00686_3_at --- ---
|
|
|
587 AFFX-18SRNAMur/X00686_5_at --- ---
|
|
|
588 AFFX-18SRNAMur/X00686_M_at --- ---
|
|
|
589
|
|
|
590 MWG_Human_30K_A.chip
|
|
|
591 Probe Set ID Gene Symbol Gene Title
|
|
|
592 1-A1 IFNA8 interferon, alpha 8
|
|
|
593 1-A10 AGL amylo-1, 6-glucosidase, 4-alpha-glucanotransferase (glycogen debranching enzyme, glycogen storage disease type III)
|
|
|
594 1-A11 NULL NULL
|
|
|
595
|
|
|
596 MWG_Human_30K_B.chip
|
|
|
597 Probe Set ID Gene Symbol Gene Title
|
|
|
598 1-A10 ADAM11 a disintegrin and metalloproteinase domain 11
|
|
|
599 1-A11 NULL NULL
|
|
|
600 1-A12 MAST3 microtubule associated serine/threonine kinase 3
|
|
|
601
|
|
|
602 Netherland_cancer_institute_operon_human_35k.chip
|
|
|
603 Probe Set ID Gene Symbol Gene Title
|
|
|
604 H200001046 ZZZ3 zinc finger, ZZ domain containing 3 [Homo sapiens]. [Source:RefSeq;Acc:NM_015534]
|
|
|
605 H200011098 ZZEF1 zinc finger, ZZ-type with EF hand domain 1 [Homo sapiens]. [Source:RefSeq;Acc:NM_015113]
|
|
|
606 H200006223 ZYX Zyxin (Zyxin 2). [Source:Uniprot/SWISSPROT;Acc:Q15942]
|
|
|
607
|
|
|
608 Netherland_cancer_institute_operon_mouse_FOOk.chip
|
|
|
609 Probe Set ID Gene Symbol Gene Title
|
|
|
610 M300012631 ZZEF1 NULL
|
|
|
611 M300012632 ZZEF1 NULL
|
|
|
612 M200002019 ZYX Zyxin. [Source:Uniprot/SWISSPROT;Acc:Q62523]
|
|
|
613
|
|
|
614 NIA15k.chip
|
|
|
615 Probe Set ID Gene Symbol Gene Title
|
|
|
616 H3051B03 BG067146 H3051B03-3 NIA Mouse 15K cDNA Clone Set Mus musculus cDNA
|
|
|
617 H3067H02 BG068648 H3067H02-3 NIA Mouse 15K cDNA Clone Set Mus musculus cDNA
|
|
|
618 H3121E03 AK029878 NULL
|
|
|
619
|
|
|
620 OPERON_HUMANv2.chip
|
|
|
621 Probe Set ID Gene Symbol Gene Title
|
|
|
622 1-A01 NULL NULL
|
|
|
623 1-A02 NULL NULL
|
|
|
624 1-A03 NAT2 N-acetyltransferase 2 (arylamine N-acetyltransferase)
|
|
|
625
|
|
|
626 OPERON_HUMANv3.chip
|
|
|
627 Probe Set ID Gene Symbol Gene Title
|
|
|
628 1-A03 TSPAN6 tetraspanin 6
|
|
|
629 1-A04 AK2 adenylate kinase 2
|
|
|
630 1-A05 NULL NULL
|
|
|
631
|
|
|
632 RAE230A.chip
|
|
|
633 Probe Set ID Gene Symbol Gene Title
|
|
|
634 1367452_at SUMO2 SMT3 suppressor of mif two 3 homolog 2 (yeast)
|
|
|
635 1367453_at CDC37 cell division cycle 37 homolog (S. cerevisiae)
|
|
|
636 1367454_at COPB2 coatomer protein complex, subunit beta 2 (beta prime)
|
|
|
637
|
|
|
638 RAE230B.chip
|
|
|
639 Probe Set ID Gene Symbol Gene Title
|
|
|
640 1367452_at SUMO2 SMT3 suppressor of mif two 3 homolog 2 (yeast)
|
|
|
641 1367453_at CDC37 cell division cycle 37 homolog (S. cerevisiae)
|
|
|
642 1367454_at COPB2 coatomer protein complex, subunit beta 2 (beta prime)
|
|
|
643
|
|
|
644 Rat230_2.chip
|
|
|
645 Probe Set ID Gene Symbol Gene Title
|
|
|
646 1367452_at SUMO2 SMT3 suppressor of mif two 3 homolog 2 (yeast)
|
|
|
647 1367453_at CDC37 cell division cycle 37 homolog (S. cerevisiae)
|
|
|
648 1367454_at COPB2 coatomer protein complex, subunit beta 2 (beta prime)
|
|
|
649
|
|
|
650 RefSeq_human.chip
|
|
|
651 Probe Set ID Gene Symbol Gene Title
|
|
|
652 NM_030625 CXXC6 CXXC finger 6
|
|
|
653 NM_181776 SLC36A2 solute carrier family 36 (proton/amino acid symporter), member 2
|
|
|
654 NM_152616 TRIM42 tripartite motif-containing 42
|
|
|
655
|
|
|
656 RefSeq_NP_Human.chip
|
|
|
657 Probe Set ID Gene Symbol Gene Title
|
|
|
658 NP_000005 A2M alpha-2-macroglobulin
|
|
|
659 NP_000006 NAT2 N-acetyltransferase 2 (arylamine N-acetyltransferase)
|
|
|
660 NP_000007 ACADM acyl-Coenzyme A dehydrogenase, C-4 to C-12 straight chain
|
|
|
661
|
|
|
662 RefSeq_NP_Mouse.chip
|
|
|
663 Probe Set ID Gene Symbol Gene Title
|
|
|
664 AAF62769 NULL NULL
|
|
|
665 AAF62770 NULL NULL
|
|
|
666 AAF62771 NULL NULL
|
|
|
667
|
|
|
668 RefSeq_NP_Rat.chip
|
|
|
669 Probe Set ID Gene Symbol Gene Title
|
|
|
670 NP_007225 NULL NULL
|
|
|
671 NP_007226 NULL NULL
|
|
|
672 NP_007227 NULL NULL
|
|
|
673
|
|
|
674 Research_Genetics.chip
|
|
|
675 Probe Set ID Gene Symbol Gene Title
|
|
|
676 1-a-1 NULL NULL
|
|
|
677 1-a-10 WNT2 wingless-type MMTV integration site family member 2
|
|
|
678 1-a-11 VHL von Hippel-Lindau tumor suppressor
|
|
|
679
|
|
|
680 RG_U34A.chip
|
|
|
681 Probe Set ID Gene Symbol Gene Title
|
|
|
682 A01157cds_s_at LIPF lipase, gastric
|
|
|
683 A03913cds_s_at SERPINE2 serine (or cysteine) proteinase inhibitor, clade E, member 2
|
|
|
684 A04674cds_s_at UCP1 uncoupling protein 1 (mitochondrial, proton carrier)
|
|
|
685
|
|
|
686 RG_U34B.chip
|
|
|
687 Probe Set ID Gene Symbol Gene Title
|
|
|
688 AFFX-BioB-3_at --- ---
|
|
|
689 AFFX-BioB-3_st --- ---
|
|
|
690 AFFX-BioB-5_at --- ---
|
|
|
691
|
|
|
692 RG_U34C.chip
|
|
|
693 Probe Set ID Gene Symbol Gene Title
|
|
|
694 AA012646_i_at --- Transcribed locus
|
|
|
695 AA012646_r_at --- Transcribed locus
|
|
|
696 AA012654_at --- Transcribed locus
|
|
|
697
|
|
|
698 RN_U34.chip
|
|
|
699 Probe Set ID Gene Symbol Gene Title
|
|
|
700 A03913cds_s_at SERPINE2 serine (or cysteine) proteinase inhibitor, clade E, member 2
|
|
|
701 A17753cds_s_at DRD3 dopamine receptor D3
|
|
|
702 AA848563_s_at HSPA1A /// HSPA1B_MAPPED heat shock 70kD protein 1A /// heat shock 70kD protein 1B (mapped)
|
|
|
703
|
|
|
704 Rosetta50K.chip
|
|
|
705 Probe Set ID Gene Symbol Gene Title
|
|
|
706 1360465 RANBP9 RAN binding protein 9
|
|
|
707 1176829 LOC375449 similar to microtubule associated testis specific serine/threonine protein kinase
|
|
|
708 1351074 NEDD4L neural precursor cell expressed, developmentally down-regulated 4-like
|
|
|
709
|
|
|
710 Rosetta.chip
|
|
|
711 Probe Set ID Gene Symbol Gene Title
|
|
|
712 NM_000504 F10 coagulation factor X
|
|
|
713 Contig32955_RC ARL6IP6 ADP-ribosylation-like factor 6 interacting protein 6
|
|
|
714 AK000455 MGC16733 hypothetical gene MGC16733 similar to CG12113
|
|
|
715
|
|
|
716 RT_U34.chip
|
|
|
717 Probe Set ID Gene Symbol Gene Title
|
|
|
718 AA108277_at HSPH1 heat shock 105kDa/110kDa protein 1
|
|
|
719 AA108308_i_at MDM2_PREDICTED Transformed mouse 3T3 cell double minute 2 homolog (mouse) (predicted)
|
|
|
720 AA108308_s_at --- ---
|
|
|
721
|
|
|
722 RZPD_Human_Ensembl1.1.chip
|
|
|
723 Probe Set ID Gene Symbol Gene Title
|
|
|
724 RZPDp203A011001D SARDH sarcosine dehydrogenase
|
|
|
725 RZPDp203A011002D ARHGAP22 Rho GTPase activating protein 22
|
|
|
726 RZPDp203A011003D CNGA3 cyclic nucleotide gated channel alpha 3
|
|
|
727
|
|
|
728 RZPD_Human_ORF_Clones_Gateway.chip
|
|
|
729 Probe Set ID Gene Symbol Gene Title
|
|
|
730 RZPDo834A0110D - Gateway (closed) PTD015 PTD015 protein
|
|
|
731 RZPDo834A0114D - Gateway (closed) TRIB3 tribbles homolog 3 (Drosophila)
|
|
|
732 RZPDo834A0116D - Gateway (closed) ORM2 orosomucoid 2
|
|
|
733
|
|
|
734 RZPD_Human_Unigene3.1.chip
|
|
|
735 Probe Set ID Gene Symbol Gene Title
|
|
|
736 HU3_p983A011001D SARDH sarcosine dehydrogenase
|
|
|
737 HU3_p983A011002D ARHGAP22 Rho GTPase activating protein 22
|
|
|
738 HU3_p983A011003D CNGA3 cyclic nucleotide gated channel alpha 3
|
|
|
739
|
|
|
740 Seq_Accession.chip
|
|
|
741 Probe Set ID Gene Symbol
|
|
|
742 AA017197 C21ORF36
|
|
|
743 AA191116 MTVR2
|
|
|
744 AA280701 CXYORF7
|
|
|
745
|
|
|
746 Stanford.chip
|
|
|
747 Probe Set ID Gene Symbol Gene Title
|
|
|
748 IMAGE:703849 DDB2 damage-specific DNA binding protein 2, 48kDa
|
|
|
749 IMAGE:1301778 ZFY zinc finger protein, Y-linked
|
|
|
750 IMAGE:795810 HS.99503HS.520681 Homo sapiens transcribed sequenceHomo sapiens, clone IMAGE:4823270, mRNA
|
|
|
751
|
|
|
752 Stanford_Source_Accessions.chip
|
|
|
753 Probe Set ID Gene Symbol Gene Title
|
|
|
754 AI848107 0610010K14RIK RIKEN cDNA 0610010K14 gene
|
|
|
755 AK002491 0610010K14RIK RIKEN cDNA 0610010K14 gene
|
|
|
756 AK003842 0610010K14RIK RIKEN cDNA 0610010K14 gene
|
|
|
757
|
|
|
758 TIGR_31K_Human_Set.chip
|
|
|
759 Probe Set ID Gene Symbol Gene Title
|
|
|
760 1-1 NULL NULL
|
|
|
761 1-10 WNT2 wingless-type MMTV integration site family member 2
|
|
|
762 1-11 VHL von Hippel-Lindau tumor suppressor
|
|
|
763
|
|
|
764 TIGR_40K_Human_Set.chip
|
|
|
765 Probe Set ID Gene Symbol Gene Title
|
|
|
766 10 NULL NULL
|
|
|
767 100 TEX27 testis expressed sequence 27
|
|
|
768 1000 HOXA1 homeo box A1
|
|
|
769
|
|
|
770 U133_X3P.chip
|
|
|
771 Probe Set ID Gene Symbol Gene Title
|
|
|
772 1053_3p_at RFC2 replication factor C (activator 1) 2, 40kDa
|
|
|
773 117_3p_at HSPA6 /// LOC652878 heat shock 70kDa protein 6 (HSP70B') /// similar to heat shock 70kDa protein 6 (HSP70B)
|
|
|
774 1494_3p_f_at CYP2A6 cytochrome P450, family 2, subfamily A, polypeptide 6
|
|
|
775
|
|
|
776 UCLA_NIH_33K.chip
|
|
|
777 Probe Set ID Gene Symbol Gene Title
|
|
|
778 1020181 NULL NULL
|
|
|
779 1020315 VAV2 vav 2 oncogene
|
|
|
780 1020478 AP1GBP1 AP1 gamma subunit binding protein 1
|
|
|
781
|
|
|
782 Zebrafish.chip
|
|
|
783 Probe Set ID Gene Symbol Gene Title
|
|
|
784 AFFX-BioB-3_at --- ---
|
|
|
785 AFFX-BioB-5_at --- ---
|
|
|
786 AFFX-BioB-M_at --- ---
|
|
|
787
|
|
|
788
|
|
|
789 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
|
|
|
790 .. _GSEA: http://www.broadinstitute.org/gsea
|
|
|
791 .. _GUIDE: http://www.broadinstitute.org/gsea/doc/GSEAUserGuideFrame.html?_Interpreting_GSEA_Results
|
|
|
792 .. _MSigDB: http://www.broadinstitute.org/gsea/msigdb/index.jsp
|
|
|
793 .. _2005Paper: http://www.pnas.org/content/102/43/15545.full
|
|
|
794
|
|
|
795 </help>
|
|
|
796
|
|
|
797 </tool>
|
|
|
798
|
|
|
799
|
