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comparison rgGSEA/rgGSEAcolumns.xml @ 2:71fa159646c9 draft

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1 <tool id="rgGSEAcolumns" name="Gene set enrichment" version="0.05">
2 <description>using a generic tabular file</description>
3 <requirements>
4 <requirement type="package" version="2.0.12">gsea</requirement>
5 <requirement type="set_environment">GSEAJAR_PATH</requirement>
6 </requirements>
7 <command interpreter="python">rgGSEA.py --input_tab "$input1" --adjpvalcol "$adjpvalcol" --signcol "$signcol"
8 --idcol "$idcol" --outhtml "$html_file" --input_name "${input1.name}"
9 --setMax "$setMax" --setMin "$setMin" --nPerm "$nPerm" --plotTop "$plotTop"
10 --gsea_jar "\$GSEAJAR_PATH"
11 --output_dir "$html_file.files_path" --mode "$mode" --title "$title"
12 #if $makeTab.value=='Yes'
13 --outtab_pos "$outtab_pos" --outtab_neg "$outtab_neg"
14 #end if
15 #if $gmtSource.refgmtSource == "indexed" or $gmtSource.refgmtSource == "both":
16 --builtin_gmt "${gmtSource.builtinGMT.fields.path}"
17 #end if
18 #if $gmtSource.refgmtSource == "history" or $gmtSource.refgmtSource == "both":
19 --history_gmt "${gmtSource.ownGMT}" --history_gmt_name "${gmtSource.ownGMT.name}"
20 #end if
21 #if $checkchip.convertchip=="yes"
22 --chip "${checkchip.use_chip.fields.path}"
23 #end if
24 </command>
25 <inputs>
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"
27 help=""/>
28 <param name="adjpvalcol" label="Column containing a p value for the DEG statistical test"
29 help = "Use RAW p-values - not FDR adjusted as these have a non GSEA friendly non-uniform distribution"
30 type="data_column" data_ref="input1" numerical="True"
31 multiple="false" use_header_names="true" size="5">
32 <validator type="no_options" message="Please select a p value column."/>
33 </param>
34 <param name="signcol" label="Column containing the DE sign - eg log fold change so positive/negative values = upregulated/downregulated in treatment"
35 type="data_column" data_ref="input1" numerical="True"
36 multiple="false" use_header_names="true" size="5">
37 <validator type="no_options" message="Please select a sign column."/>
38 </param>
39 <param name="idcol" label="Column containing a gene id (refseq, symbol or Entrez"
40 type="data_column" data_ref="input1" numerical="False"
41 multiple="false" use_header_names="true" size="5">
42 <validator type="no_options" message="Please select an id column."/>
43 </param>
44
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"/>
46 <param name="setMin" type="integer" label="Minimum gene set size to prune (default=15)" size="5" value="15"/>
47 <param name="setMax" type="integer" label="Maximum gene set size to prune (default=500)" size="5" value="500"/>
48 <param name="nPerm" type="integer" label="Number of permutations (default=1000)" size="7" value="1000"/>
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"/>
50 <param name="mode" type="select" label="Mode for dealing with duplicated gene ids" >
51 <option value="Max_probe" selected="true">Use the most extreme value</option>
52 <option value="Median_of_probes">Use the median of all supplied values</option>
53 </param>
54 <param name="makeTab" type="select" label="Create a tabular report containing ALL gene sets for downstream analysis" >
55 <option value="Yes">Yes</option>
56 <option value="No" selected="true">No</option>
57 </param>
58 <conditional name="checkchip" >
59 <param name="convertchip" type="select" label="Translate the rank file IDs (first column) using a GSEA 'chip' lookup table">
60 <option value="yes">Use a GSEA 'chip' file</option>
61 <option value="no" selected="true">IDs are already gene symbols - no translation needed </option>
62 </param>
63 <when value="no">
64 </when>
65 <when value="yes">
66 <param name="use_chip" type="select" label="Select a GSEA 'chip' for the probe ids or symbols in the ranks file">
67 <options from_data_table="gseaChip_3.1">
68 <filter type="sort_by" column="2" />
69 <validator type="no_options" message="No chip tables are available - please see the Galaxy GSEA tool documentation for instructions on installing them" />
70 </options>
71 </param>
72 </when>
73 </conditional>
74 <conditional name="gmtSource">
75 <param name="refgmtSource" type="select" label="Use a gene set (.gmt) from your history or use a built-in (MSigDB etc) gene set">
76 <option value="indexed" selected="true">Use a built-in gene set</option>
77 <option value="history">Use a gene set from my history</option>
78 <option value="both">Add a gene set from my history to a built in gene set</option>
79 </param>
80 <when value="indexed">
81 <param name="builtinGMT" type="select" label="Select a gene set matrix (.gmt) file to use for the analysis">
82 <options from_data_table="gseaGMT_3.1">
83 <filter type="sort_by" column="2" />
84 <validator type="no_options" message="No GMT v3.1 files are available - please install them"/>
85 </options>
86 </param>
87 </when>
88 <when value="history">
89 <param name="ownGMT" type="data" format="gmt" label="Select a Gene Set from your history" />
90 </when>
91 <when value="both">
92 <param name="ownGMT" type="data" format="gmt" label="Select a Gene Set from your history" />
93 <param name="builtinGMT" type="select" label="Select a gene set matrix (.gmt) file to use for the analysis">
94 <options from_data_table="gseaGMT_3.1">
95 <filter type="sort_by" column="2" />
96 <validator type="no_options" message="No GMT v3.1 files are available - please install them"/>
97 </options>
98 </param>
99 </when>
100 </conditional>
101 </inputs>
102 <outputs>
103 <data format="html" name="html_file" label="${title}.html"/>
104 <data format="tabular" name="outtab_pos" label="${title}_pos_allsets.xls">
105 <filter>makeTab=="Yes"</filter>
106 </data>
107 <data format="tabular" name="outtab_neg" label="${title}_neg_allsets.xls">
108 <filter>makeTab=="Yes"</filter>
109 </data>
110
111 </outputs>
112 <help>
113 **What it does**
114
115 Performs Gene set enrichment analysis using GSEA_ from the Broad as described in 2005Paper_ and v3.1 of msigdb
116
117 Refer to http://www.pnas.org/cgi/content/abstract/0506580102v1 for details of the method.
118
119 **Input**
120
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
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
123 or some other valid analysis.
124 Probe names can be translated using the chip file option (see below)
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
126
127 **Gene sets**
128
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.
130
131 Alternatively, use one of the built in MSigDB_ (molecular signatures database) sets.
132 There may be additional locally provided sets such as starBase
133
134 Optionally, a local gmt can be merged with a built in one if you want to see how they perform competitively
135
136 Select the most appropriate subset of MSigDB gene sets or use all by choosing msigdb.v3.0.symbols.
137 A non-cancer subset called c2_c3_c5_all.v3.0.symbols is recommended if you are working with non-cancer biology.
138
139
140 **Chip**
141
142 If your input file contains HUGO gene symbols (TEK, SLC38A1...etc) then you do not need to specify a 'chip'.
143
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
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.
146
147 **Output**
148
149 A report as html - see the GUIDE_ for a guide on interpretation
150
151
152 **Attribution**
153
154 This Galaxy tool wrapper was written by Ross Lazarus.
155 It executes the GSEA_ java application available using MSigDB and Chip files obtained from the GSEA_ web site
156
157
158 **Chip ID samples**
159
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
161
162 ::
163
164 AG.chip
165 Probe Set ID Gene Symbol Gene Title
166 11986_at --- calcium-dependent lipid-binding protein, putative
167 11987_at --- zinc finger (C3HC4-type RING finger) family protein
168 11988_at --- WD-40 repeat family protein
169
170 Agilent_Human1A.chip
171 Probe Set ID Gene Symbol Gene Title
172 A_23_P100001 LOC400451 hypothetical gene supported by AK075564; BC060873
173 A_23_P100011 AP3S2 adaptor-related protein complex 3, sigma 2 subunit
174 A_23_P10002 CEP63 centrosome protein Cep63
175
176 Agilent_Human1Av2.chip
177 Probe Set ID Gene Symbol Gene Title
178 A_23_P100001 LOC400451 hypothetical gene supported by AK075564; BC060873
179 A_23_P100011 AP3S2 adaptor-related protein complex 3, sigma 2 subunit
180 A_23_P10002 CEP63 centrosome protein Cep63
181
182 Agilent_Human1B.chip
183 Probe Set ID Gene Symbol Gene Title
184 A_32_P10002 TUBA2 tubulin, alpha 2
185 A_32_P100076 RPL19 ribosomal protein L19
186 A_32_P100100 THOC3 THO complex 3
187
188 Agilent_Human1_cDNA.chip
189 Probe Set ID Gene Symbol Gene Title
190 1 RNASEH2A ribonuclease H2, large subunit
191 10 SF3B1 splicing factor 3b, subunit 1, 155kDa
192 100 S100A16 S100 calcium binding protein A16
193
194 Agilent_HumanGenome.chip
195 Probe Set ID Gene Symbol Gene Title
196 A_23_P100001 LOC400451 hypothetical gene supported by AK075564; BC060873
197 A_23_P100011 NULL NULL
198 A_23_P100022 SV2B synaptic vesicle glycoprotein 2B
199
200 Agilent_Mouse_cDNA.chip
201 Probe Set ID Gene Symbol Gene Title
202 1000982 SLC6A9 solute carrier family 6 (neurotransmitter transporter, glycine), member 9
203 1001007 IGF1 insulin-like growth factor 1
204 1001011 FCNA ficolin A
205
206 Agilent_MouseDev.chip
207 Probe Set ID Gene Symbol Gene Title
208 A_65_P00523 NULL NULL
209 A_65_P00524 NULL NULL
210 A_65_P00525 SFTPD surfactant associated protein D
211
212 Agilent_MouseGenome.chip
213 Probe Set ID Gene Symbol Gene Title
214 A_51_P100021 NULL NULL
215 A_51_P100034 2310075G12RIK RIKEN cDNA 2310075G12 gene
216 A_51_P100052 SLITRK2 SLIT and NTRK-like family, member 2
217
218 Agilent_MouseOligo.chip
219 Probe Set ID Gene Symbol Gene Title
220 A_51_P100021 NULL NULL
221 A_51_P100034 2310075G12RIK RIKEN cDNA 2310075G12 gene
222 A_51_P100052 SLITRK2 SLIT and NTRK-like family, member 2
223
224 Agilent_RatGenome_G4131A.chip
225 Probe Set ID Gene Symbol Gene Title
226 A_42_P453055 LU Lutheran blood group (Auberger b antigen included)
227 A_42_P453737 NULL NULL
228 A_42_P453894 RGD1306682_PREDICTED similar to RIKEN cDNA 1810046J19 (predicted)
229
230 Agilent_RatOligo.chip
231 Probe Set ID Gene Symbol Gene Title
232 A_42_P453131 CNTN1 contactin 1
233 A_42_P453151 TTC8_PREDICTED tetratricopeptide repeat domain 8 (predicted)
234 A_42_P453162 NULL NULL
235
236 APPLERA_ABI1700.chip
237 Probe Set ID Gene Symbol Gene Title
238 100002 NULL NULL
239 100003 NULL NULL
240 100027 ZNF192 zinc finger protein 192
241
242 ATH1_121501.chip
243 Probe Set ID Gene Symbol Gene Title
244 244901_at --- ---
245 244902_at --- ---
246 244903_at --- ---
247
248 AtlasMouse1.2.chip
249 Probe Set ID Gene Symbol Gene Title
250 MA099 HTR1A 5-hydroxytryptamine (serotonin) receptor 1A
251 MA015 JARID2 jumonji, AT rich interactive domain 2
252 M443 CDKN2C cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)
253
254 AtlasRat1.2.chip
255 Probe Set ID Gene Symbol Gene Title
256 R484 TPP2 tripeptidylpeptidase II
257 RG348 MOS v-mos moloney murine sarcoma viral oncogene homolog
258 RG119 KCNJ1 potassium inwardly-rectifying channel, subfamily J, member 1
259
260 Bovine.chip
261 Probe Set ID Gene Symbol Gene Title
262 AFFX-BioB-3_at --- ---
263 AFFX-BioB-5_at --- ---
264 AFFX-BioB-M_at --- ---
265
266 Caltech16KMouse.chip
267 Probe Set ID Gene Symbol Gene Title
268 6712 CCL6 chemokine (C-C motif) ligand 6
269 8563 ACTL7B actin-like 7b
270 8434 1700049M11RIK RIKEN cDNA 1700049M11 gene
271
272 Caltech16KOligoMouse.chip
273 Probe Set ID Gene Symbol Gene Title
274 6712 GCA grancalcin, EF-hand calcium binding protein
275 8563 MARVELD2 MARVEL (membrane-associating) domain containing 2
276 8434 BC048825 NULL
277
278 Canine_2.chip
279 Probe Set ID Gene Symbol Gene Title
280 AFFX-BioB-3_at --- ---
281 AFFX-BioB-5_at --- ---
282 AFFX-BioB-M_at --- ---
283
284 Clontech_Atlas_13K.chip
285 Probe Set ID Gene Symbol Gene Title
286 1-A01 NULL NULL
287 1-A02 A2M alpha-2-macroglobulin
288 1-A03 AADAC arylacetamide deacetylase (esterase)
289
290 Clontech_BD_Atlas.chip
291 Probe Set ID Gene Symbol Gene Title
292 A01a PCP4 Purkinje cell protein 4
293 A01b NULL NULL
294 A01c PMP22 peripheral myelin protein
295
296 CNMCMuscleChip.chip
297 Probe Set ID Gene Symbol Gene Title
298 HSPD4570_at MBP myelin basic protein
299 HSPD7328_at MAPK12 mitogen-activated protein kinase 12
300 HSPD17028_i_at DIA1 diaphorase (NADH) (cytochrome b-5 reductase)
301
302 CodeLink_Human_Whole_Genome.chip
303 Probe Set ID Gene Symbol Gene Title
304 GE469530 NULL NULL
305 GE469548 TMEM1 transmembrane protein 1
306 GE469549 NULL NULL
307
308 CodeLink_UniSet_Human_20K_I_Bioarray.chip
309 Probe Set ID Gene Symbol Gene Title
310 000106CB1_PROBE1 NDUFA4 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4, 9kDa
311 000136CB1_PROBE1 MRPS33 mitochondrial ribosomal protein S33
312 000278CB1_PROBE1 FDFT1 farnesyl-diphosphate farnesyltransferase 1
313
314 CodeLink_UniSet_Human_I_Bioarray.chip
315 Probe Set ID Gene Symbol Gene Title
316 AA001334_PROBE1 ZHX2 zinc fingers and homeoboxes 2
317 AA002191_PROBE1 PITPNA phosphatidylinositol transfer protein, alpha
318 AA004381_PROBE1 NULL NULL
319
320 CodeLink_UniSet_Human_II_Bioarray.chip
321 Probe Set ID Gene Symbol Gene Title
322 000106CB1_PROBE1 NDUFA4 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4, 9kDa
323 000136CB1_PROBE1 MRPS33 mitochondrial ribosomal protein S33
324 000278CB1_PROBE1 FDFT1 farnesyl-diphosphate farnesyltransferase 1
325
326 CodeLink_UniSet_Rat_I_Bioarray.chip
327 Probe Set ID Gene Symbol Gene Title
328 AA799301_PROBE1 NULL NULL
329 AA799313_PROBE1 RGD:1303279 sialyltransferase 10 (alpha-2,3-sialyltransferase VI)
330 AA799329_PROBE1 NULL NULL
331
332 DrosGenome1.chip
333 Probe Set ID Gene Symbol Gene Title
334 141200_at CG9418 CG9418
335 141201_at CG17840 CG17840
336 141202_at QKR58E-3 quaking related 58E-3
337
338 Drosophila_2.chip
339 Probe Set ID Gene Symbol Gene Title
340 1616608_a_at GPDH Glycerol 3 phosphate dehydrogenase
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