Mercurial > repos > fubar > rg_gsea
diff rgGSEA/rgGSEAcolumns.xml @ 2:71fa159646c9 draft
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| author | fubar |
|---|---|
| date | Sun, 09 Jun 2013 02:01:13 -0400 |
| parents | |
| children | 8e291f464aa0 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgGSEA/rgGSEAcolumns.xml Sun Jun 09 02:01:13 2013 -0400 @@ -0,0 +1,799 @@ +<tool id="rgGSEAcolumns" name="Gene set enrichment" version="0.05"> + <description>using a generic tabular file</description> + <requirements> + <requirement type="package" version="2.0.12">gsea</requirement> + <requirement type="set_environment">GSEAJAR_PATH</requirement> + </requirements> + <command interpreter="python">rgGSEA.py --input_tab "$input1" --adjpvalcol "$adjpvalcol" --signcol "$signcol" + --idcol "$idcol" --outhtml "$html_file" --input_name "${input1.name}" + --setMax "$setMax" --setMin "$setMin" --nPerm "$nPerm" --plotTop "$plotTop" + --gsea_jar "\$GSEAJAR_PATH" + --output_dir "$html_file.files_path" --mode "$mode" --title "$title" +#if $makeTab.value=='Yes' + --outtab_pos "$outtab_pos" --outtab_neg "$outtab_neg" +#end if +#if $gmtSource.refgmtSource == "indexed" or $gmtSource.refgmtSource == "both": +--builtin_gmt "${gmtSource.builtinGMT.fields.path}" +#end if +#if $gmtSource.refgmtSource == "history" or $gmtSource.refgmtSource == "both": +--history_gmt "${gmtSource.ownGMT}" --history_gmt_name "${gmtSource.ownGMT.name}" +#end if +#if $checkchip.convertchip=="yes" + --chip "${checkchip.use_chip.fields.path}" +#end if +</command> + <inputs> + <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" + help=""/> + <param name="adjpvalcol" label="Column containing a p value for the DEG statistical test" + help = "Use RAW p-values - not FDR adjusted as these have a non GSEA friendly non-uniform distribution" + type="data_column" data_ref="input1" numerical="True" + multiple="false" use_header_names="true" size="5"> + <validator type="no_options" message="Please select a p value column."/> + </param> + <param name="signcol" label="Column containing the DE sign - eg log fold change so positive/negative values = upregulated/downregulated in treatment" + type="data_column" data_ref="input1" numerical="True" + multiple="false" use_header_names="true" size="5"> + <validator type="no_options" message="Please select a sign column."/> + </param> + <param name="idcol" label="Column containing a gene id (refseq, symbol or Entrez" + type="data_column" data_ref="input1" numerical="False" + multiple="false" use_header_names="true" size="5"> + <validator type="no_options" message="Please select an id column."/> + </param> + + <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"/> + <param name="setMin" type="integer" label="Minimum gene set size to prune (default=15)" size="5" value="15"/> + <param name="setMax" type="integer" label="Maximum gene set size to prune (default=500)" size="5" value="500"/> + <param name="nPerm" type="integer" label="Number of permutations (default=1000)" size="7" value="1000"/> + <param name="plotTop" type="integer" label="Number of top gene sets to plot and present in detailed reports(default=20)" size="10" value="20"/> + <param name="mode" type="select" label="Mode for dealing with duplicated gene ids" > + <option value="Max_probe" selected="true">Use the most extreme value</option> + <option value="Median_of_probes">Use the median of all supplied values</option> + </param> + <param name="makeTab" type="select" label="Create a tabular report containing ALL gene sets for downstream analysis" > + <option value="Yes">Yes</option> + <option value="No" selected="true">No</option> + </param> + <conditional name="checkchip" > + <param name="convertchip" type="select" label="Translate the rank file IDs (first column) using a GSEA 'chip' lookup table"> + <option value="yes">Use a GSEA 'chip' file</option> + <option value="no" selected="true">IDs are already gene symbols - no translation needed </option> + </param> + <when value="no"> + </when> + <when value="yes"> + <param name="use_chip" type="select" label="Select a GSEA 'chip' for the probe ids or symbols in the ranks file"> + <options from_data_table="gseaChip_3.1"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No chip tables are available - please see the Galaxy GSEA tool documentation for instructions on installing them" /> + </options> + </param> + </when> + </conditional> + <conditional name="gmtSource"> + <param name="refgmtSource" type="select" label="Use a gene set (.gmt) from your history 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="gmt" 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_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> + </conditional> + </inputs> + <outputs> + <data format="html" name="html_file" label="${title}.html"/> + <data format="tabular" name="outtab_pos" label="${title}_pos_allsets.xls"> + <filter>makeTab=="Yes"</filter> + </data> + <data format="tabular" name="outtab_neg" label="${title}_neg_allsets.xls"> + <filter>makeTab=="Yes"</filter> + </data> + + </outputs> +<help> +**What it does** + +Performs Gene set enrichment analysis using GSEA_ from the Broad as described in 2005Paper_ and v3.1 of msigdb + +Refer to http://www.pnas.org/cgi/content/abstract/0506580102v1 for details of the method. + +**Input** + +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 +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 +or some other valid analysis. +Probe names can be translated using the chip file option (see below) +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 + +**Gene sets** + +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. + +Alternatively, use one of the built in MSigDB_ (molecular signatures database) sets. +There may be additional locally provided sets such as starBase + +Optionally, a local gmt can be merged with a built in one if you want to see how they perform competitively + +Select the most appropriate subset of MSigDB gene sets or use all by choosing msigdb.v3.0.symbols. +A non-cancer subset called c2_c3_c5_all.v3.0.symbols is recommended if you are working with non-cancer biology. + + +**Chip** + +If your input file contains HUGO gene symbols (TEK, SLC38A1...etc) then you do not need to specify a 'chip'. + +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 +Failure to match the translation correctly will generally result in failure of the job since none of your input data will be translated properly. + +**Output** + +A report as html - see the GUIDE_ for a guide on interpretation + + +**Attribution** + +This Galaxy tool wrapper was written by Ross Lazarus. +It executes the GSEA_ java application available using MSigDB and Chip files obtained from the GSEA_ web site + + +**Chip ID samples** + +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 + + :: + + AG.chip + Probe Set ID Gene Symbol Gene Title + 11986_at --- calcium-dependent lipid-binding protein, putative + 11987_at --- zinc finger (C3HC4-type RING finger) family protein + 11988_at --- WD-40 repeat family protein + + Agilent_Human1A.chip + Probe Set ID Gene Symbol Gene Title + A_23_P100001 LOC400451 hypothetical gene supported by AK075564; BC060873 + A_23_P100011 AP3S2 adaptor-related protein complex 3, sigma 2 subunit + A_23_P10002 CEP63 centrosome protein Cep63 + + Agilent_Human1Av2.chip + Probe Set ID Gene Symbol Gene Title + A_23_P100001 LOC400451 hypothetical gene supported by AK075564; BC060873 + A_23_P100011 AP3S2 adaptor-related protein complex 3, sigma 2 subunit + A_23_P10002 CEP63 centrosome protein Cep63 + + Agilent_Human1B.chip + Probe Set ID Gene Symbol Gene Title + A_32_P10002 TUBA2 tubulin, alpha 2 + A_32_P100076 RPL19 ribosomal protein L19 + A_32_P100100 THOC3 THO complex 3 + + Agilent_Human1_cDNA.chip + Probe Set ID Gene Symbol Gene Title + 1 RNASEH2A ribonuclease H2, large subunit + 10 SF3B1 splicing factor 3b, subunit 1, 155kDa + 100 S100A16 S100 calcium binding protein A16 + + Agilent_HumanGenome.chip + Probe Set ID Gene Symbol Gene Title + A_23_P100001 LOC400451 hypothetical gene supported by AK075564; BC060873 + A_23_P100011 NULL NULL + A_23_P100022 SV2B synaptic vesicle glycoprotein 2B + + Agilent_Mouse_cDNA.chip + Probe Set ID Gene Symbol Gene Title + 1000982 SLC6A9 solute carrier family 6 (neurotransmitter transporter, glycine), member 9 + 1001007 IGF1 insulin-like growth factor 1 + 1001011 FCNA ficolin A + + Agilent_MouseDev.chip + Probe Set ID Gene Symbol Gene Title + A_65_P00523 NULL NULL + A_65_P00524 NULL NULL + A_65_P00525 SFTPD surfactant associated protein D + + Agilent_MouseGenome.chip + Probe Set ID Gene Symbol Gene Title + A_51_P100021 NULL NULL + A_51_P100034 2310075G12RIK RIKEN cDNA 2310075G12 gene + A_51_P100052 SLITRK2 SLIT and NTRK-like family, member 2 + + Agilent_MouseOligo.chip + Probe Set ID Gene Symbol Gene Title + A_51_P100021 NULL NULL + A_51_P100034 2310075G12RIK RIKEN cDNA 2310075G12 gene + A_51_P100052 SLITRK2 SLIT and NTRK-like family, member 2 + + Agilent_RatGenome_G4131A.chip + Probe Set ID Gene Symbol Gene Title + A_42_P453055 LU Lutheran blood group (Auberger b antigen included) + A_42_P453737 NULL NULL + A_42_P453894 RGD1306682_PREDICTED similar to RIKEN cDNA 1810046J19 (predicted) + + Agilent_RatOligo.chip + Probe Set ID Gene Symbol Gene Title + A_42_P453131 CNTN1 contactin 1 + A_42_P453151 TTC8_PREDICTED tetratricopeptide repeat domain 8 (predicted) + A_42_P453162 NULL NULL + + APPLERA_ABI1700.chip + Probe Set ID Gene Symbol Gene Title + 100002 NULL NULL + 100003 NULL NULL + 100027 ZNF192 zinc finger protein 192 + + ATH1_121501.chip + Probe Set ID Gene Symbol Gene Title + 244901_at --- --- + 244902_at --- --- + 244903_at --- --- + + AtlasMouse1.2.chip + Probe Set ID Gene Symbol Gene Title + MA099 HTR1A 5-hydroxytryptamine (serotonin) receptor 1A + MA015 JARID2 jumonji, AT rich interactive domain 2 + M443 CDKN2C cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4) + + AtlasRat1.2.chip + Probe Set ID Gene Symbol Gene Title + R484 TPP2 tripeptidylpeptidase II + RG348 MOS v-mos moloney murine sarcoma viral oncogene homolog + RG119 KCNJ1 potassium inwardly-rectifying channel, subfamily J, member 1 + + Bovine.chip + Probe Set ID Gene Symbol Gene Title + AFFX-BioB-3_at --- --- + AFFX-BioB-5_at --- --- + AFFX-BioB-M_at --- --- + + Caltech16KMouse.chip + Probe Set ID Gene Symbol Gene Title + 6712 CCL6 chemokine (C-C motif) ligand 6 + 8563 ACTL7B actin-like 7b + 8434 1700049M11RIK RIKEN cDNA 1700049M11 gene + + Caltech16KOligoMouse.chip + Probe Set ID Gene Symbol Gene Title + 6712 GCA grancalcin, EF-hand calcium binding protein + 8563 MARVELD2 MARVEL (membrane-associating) domain containing 2 + 8434 BC048825 NULL + + Canine_2.chip + Probe Set ID Gene Symbol Gene Title + AFFX-BioB-3_at --- --- + AFFX-BioB-5_at --- --- + AFFX-BioB-M_at --- --- + + Clontech_Atlas_13K.chip + Probe Set ID Gene Symbol Gene Title + 1-A01 NULL NULL + 1-A02 A2M alpha-2-macroglobulin + 1-A03 AADAC arylacetamide deacetylase (esterase) + + Clontech_BD_Atlas.chip + Probe Set ID Gene Symbol Gene Title + A01a PCP4 Purkinje cell protein 4 + A01b NULL NULL + A01c PMP22 peripheral myelin protein + + CNMCMuscleChip.chip + Probe Set ID Gene Symbol Gene Title + HSPD4570_at MBP myelin basic protein + HSPD7328_at MAPK12 mitogen-activated protein kinase 12 + HSPD17028_i_at DIA1 diaphorase (NADH) (cytochrome b-5 reductase) + + CodeLink_Human_Whole_Genome.chip + Probe Set ID Gene Symbol Gene Title + GE469530 NULL NULL + GE469548 TMEM1 transmembrane protein 1 + GE469549 NULL NULL + + CodeLink_UniSet_Human_20K_I_Bioarray.chip + Probe Set ID Gene Symbol Gene Title + 000106CB1_PROBE1 NDUFA4 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4, 9kDa + 000136CB1_PROBE1 MRPS33 mitochondrial ribosomal protein S33 + 000278CB1_PROBE1 FDFT1 farnesyl-diphosphate farnesyltransferase 1 + + CodeLink_UniSet_Human_I_Bioarray.chip + Probe Set ID Gene Symbol Gene Title + AA001334_PROBE1 ZHX2 zinc fingers and homeoboxes 2 + AA002191_PROBE1 PITPNA phosphatidylinositol transfer protein, alpha + AA004381_PROBE1 NULL NULL + + CodeLink_UniSet_Human_II_Bioarray.chip + Probe Set ID Gene Symbol Gene Title + 000106CB1_PROBE1 NDUFA4 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4, 9kDa + 000136CB1_PROBE1 MRPS33 mitochondrial ribosomal protein S33 + 000278CB1_PROBE1 FDFT1 farnesyl-diphosphate farnesyltransferase 1 + + CodeLink_UniSet_Rat_I_Bioarray.chip + Probe Set ID Gene Symbol Gene Title + AA799301_PROBE1 NULL NULL + AA799313_PROBE1 RGD:1303279 sialyltransferase 10 (alpha-2,3-sialyltransferase VI) + AA799329_PROBE1 NULL NULL + + DrosGenome1.chip + Probe Set ID Gene Symbol Gene Title + 141200_at CG9418 CG9418 + 141201_at CG17840 CG17840 + 141202_at QKR58E-3 quaking related 58E-3 + + Drosophila_2.chip + Probe Set ID Gene Symbol Gene Title + 1616608_a_at GPDH Glycerol 3 phosphate dehydrogenase + 1622892_s_at CG33057 /// MKG-P CG33057 /// monkey king protein + 1622893_at IM3 /// RPS10B Immune induced molecule 3 /// Ribosomal protein S10b + + G4110A.chip + Probe Set ID Gene Symbol Gene Title + A_23_P7033 MAGEF1 melanoma antigen, family F, 1 + A_23_P170713 A_23_P170713 ***description missing*** + A_23_P107801 FLJ21742 hypothetical protein FLJ21742 + + G4110Av2.chip + Probe Set ID Gene Symbol Gene Title + A_23_P7033 MAGEF1 melanoma antigen, family F, 1 + A_23_P170713 A_23_P170713 No description available + A_23_P107801 FLJ21742 hypothetical protein FLJ21742 + + GENE_SYMBOL.chip + Probe Set ID Gene Symbol Gene Title Aliases + A1BG A1BG alpha-1-B glycoprotein GABDKFZP686F0970ABGHYST2477A1B + A2M A2M alpha-2-macroglobulin DKFZP779B086S863-7ALPHA 2MFWP007CPAMD5 + A2ML1 A2ML1 alpha-2-macroglobulin-like 1 FLJ39129DKFZP686O1010FLJ41598DKFZP686G1812FLJ25179CPAMD9DKFZP686D2011FLJ16045FLJ41607DKFZP686C1729FLJ41597DKFZP686L1821 + + GenosysCytokineV2.chip + Probe Set ID Gene Symbol Gene Title + M05.2 GDF11 growth differentiation factor 11 + M22.2 AE000170 No description available + E06.3 IL5 interleukin 5 (colony-stimulating factor, eosinophil) + + HC_G110.chip + Probe Set ID Gene Symbol Gene Title + 1000_at MAPK3 mitogen-activated protein kinase 3 + 1001_at TIE1 tyrosine kinase with immunoglobulin-like and EGF-like domains 1 + 1002_f_at CYP2C19 cytochrome P450, family 2, subfamily C, polypeptide 19 + + HG_Focus.chip + Probe Set ID Gene Symbol Gene Title + 1007_s_at DDR1 discoidin domain receptor family, member 1 + 1053_at RFC2 replication factor C (activator 1) 2, 40kDa + 117_at HSPA6 /// LOC652878 heat shock 70kDa protein 6 (HSP70B') /// similar to heat shock 70kDa protein 6 (HSP70B) + + HG_U133A_2.chip + Probe Set ID Gene Symbol Gene Title + 1007_s_at DDR1 discoidin domain receptor family, member 1 + 1053_at RFC2 replication factor C (activator 1) 2, 40kDa + 117_at HSPA6 /// LOC652878 heat shock 70kDa protein 6 (HSP70B') /// similar to heat shock 70kDa protein 6 (HSP70B) + + HG_U133AAofAv2.chip + Probe Set ID Gene Symbol Gene Title + 1007_s_at DDR1 discoidin domain receptor family, member 1 + 1053_at RFC2 replication factor C (activator 1) 2, 40kDa + 117_at HSPA6 /// LOC652878 heat shock 70kDa protein 6 (HSP70B') /// similar to heat shock 70kDa protein 6 (HSP70B) + + HG_U133A.chip + Probe Set ID Gene Symbol Gene Title + 1007_s_at DDR1 discoidin domain receptor family, member 1 + 1053_at RFC2 replication factor C (activator 1) 2, 40kDa + 117_at HSPA6 /// LOC652878 heat shock 70kDa protein 6 (HSP70B') /// similar to heat shock 70kDa protein 6 (HSP70B) + + HG_U133B.chip + Probe Set ID Gene Symbol Gene Title + 200000_s_at PRPF8 PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae) /// PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae) + 200001_at CAPNS1 calpain, small subunit 1 /// calpain, small subunit 1 + 200002_at RPL35 ribosomal protein L35 /// ribosomal protein L35 + + HG_U133_Plus_2.chip + Probe Set ID Gene Symbol Gene Title + 1007_s_at DDR1 discoidin domain receptor family, member 1 + 1053_at RFC2 replication factor C (activator 1) 2, 40kDa + 117_at HSPA6 /// LOC652878 heat shock 70kDa protein 6 (HSP70B') /// similar to heat shock 70kDa protein 6 (HSP70B) + + HG_U95Av2.chip + Probe Set ID Gene Symbol Gene Title + 1000_at MAPK3 mitogen-activated protein kinase 3 + 1001_at TIE1 tyrosine kinase with immunoglobulin-like and EGF-like domains 1 + 1002_f_at CYP2C19 cytochrome P450, family 2, subfamily C, polypeptide 19 + + HG_U95B.chip + Probe Set ID Gene Symbol Gene Title + 41880_at --- Transcribed locus + 41881_at FLJ40142 FLJ40142 protein + 41882_at FBXO42 F-box protein 42 + + HG_U95C.chip + Probe Set ID Gene Symbol Gene Title + 48609_r_at KIAA1333 KIAA1333 + 48610_at C20ORF102 chromosome 20 open reading frame 102 + 48612_at N4BP1 /// LOC653213 Nedd4 binding protein 1 /// similar to Nedd4 binding protein 1 + + HG_U95D.chip + Probe Set ID Gene Symbol Gene Title + 67020_at --- Transcribed locus + 67021_at FAM44B Family with sequence similarity 44, member B + 67023_at --- Transcribed locus + + HG_U95E.chip + Probe Set ID Gene Symbol Gene Title + 67022_at PIP5K2B Phosphatidylinositol-4-phosphate 5-kinase, type II, beta + 67024_at CASD1 CAS1 domain containing 1 + 67026_at NFASC neurofascin homolog (chicken) + + HPCGGCompugenAnnotations.chip + Probe Set ID Gene Symbol Gene Title + MGI:1913066 SH3MD2 Sh3md2, SH3 multiple domains 2 + MGI:1913099 5430413I02RIK 5430413I02Rik, RIKEN cDNA 5430413I02 gene + MGI:98848 TSHB Tshb, thyroid stimulating hormone, beta subunit + + HT_HG_U133A.chip + Probe Set ID Gene Symbol Gene Title + 1007_s_at DDR1 discoidin domain receptor family, member 1 + 1053_at RFC2 replication factor C (activator 1) 2, 40kDa + 117_at HSPA6 /// LOC652878 heat shock 70kDa protein 6 (HSP70B') /// similar to heat shock 70kDa protein 6 (HSP70B) + + Hu35KsubA.chip + Probe Set ID Gene Symbol Gene Title + AA000993_at PRDM8 PR domain containing 8 + AA001296_s_at PHF23 PHD finger protein 23 + AA002245_at ZC3H11A zinc finger CCCH-type containing 11A + + Hu35KsubB.chip + Probe Set ID Gene Symbol Gene Title + AFFX-BioB-3_at --- --- + AFFX-BioB-3_st --- --- + AFFX-BioB-5_at --- --- + + Hu35KsubC.chip + Probe Set ID Gene Symbol Gene Title + AFFX-BioB-3_at --- --- + AFFX-BioB-3_st --- --- + AFFX-BioB-5_at --- --- + + Hu35KsubD.chip + Probe Set ID Gene Symbol Gene Title + AFFX-BioB-3_at --- --- + AFFX-BioB-3_st --- --- + AFFX-BioB-5_at --- --- + + Hu6800.chip + Probe Set ID Gene Symbol Gene Title + A28102_at GABRA3 gamma-aminobutyric acid (GABA) A receptor, alpha 3 + AB000114_at OMD osteomodulin + AB000115_at IFI44L interferon-induced protein 44-like + + Illumina_Human.chip + Probe Set ID Gene Symbol Gene Title + 1-A-1 BCAP31 B-cell receptor-associated protein 31 + 1-A-10 NSFL1C NSFL1 (p97) cofactor (p47) + 1-A-11 C20ORF24 chromosome 20 open reading frame 24 + + ilmn_HumanHT_12_V4_0_R1_15002873_B.chip + Probe Set ID Gene Symbol Gene Title Entrez Gene ID + ILMN_1725881 LOC23117 PREDICTED: Homo sapiens KIAA0220-like protein, transcript variant 11 (LOC23117), mRNA. 23117 + ILMN_1910180 Homo sapiens cDNA: FLJ21027 fis, clone CAE07110 -999 + ILMN_1804174 FCGR2B PREDICTED: Homo sapiens Fc fragment of IgG, low affinity IIb, receptor (CD32) (FCGR2B), mRNA. 2213 + + ilmn_MouseRef_8_V2_0_R3_11278551_A.chip + Probe Set ID Gene Symbol Gene Title Entrez Gene ID + ILMN_2607609 YIF1B Mus musculus Yip1 interacting factor homolog B (S. cerevisiae) (Yif1b), mRNA. 77254 + ILMN_1238674 2700007P21RIK Mus musculus RIKEN cDNA 2700007P21 gene (2700007P21Rik), transcript variant 2, mRNA. 212772 + ILMN_3062534 2700007P21RIK Mus musculus RIKEN cDNA 2700007P21 gene (2700007P21Rik), transcript variant 2, mRNA. 212772 + + ilmn_MouseWG_6_V2_0_R3_11278593_A.chip + Probe Set ID Gene Symbol Gene Title Entrez Gene ID + ILMN_1243094 THRSP NULL -999 + ILMN_1238674 2700007P21RIK Mus musculus RIKEN cDNA 2700007P21 gene (2700007P21Rik), transcript variant 2, mRNA. 212772 + ILMN_2454720 2700007P21RIK Mus musculus RIKEN cDNA 2700007P21 gene (2700007P21Rik), transcript variant 2, mRNA. 212772 + + labonweb_human.chip + Probe Set ID Gene Symbol Gene Title + 1-A1 GAPD glyceraldehyde-3-phosphate dehydrogenase + 1-A10 BMP5 bone morphogenetic protein 5 + 1-A11 C9ORF78 chromosome 9 open reading frame 78 + + lymphochip.chip + Probe Set ID Gene Symbol Gene Title + 1317148 TNF tumor necrosis factor (TNF superfamily, member 2) + 814251 SLAMF1 signaling lymphocytic activation molecule family member 1 + 712899___1 AA282233 zt12d02.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone + + MG_U74Av2.chip + Probe Set ID Gene Symbol Gene Title + 100001_at CD3G CD3 antigen, gamma polypeptide + 100002_at ITIH3 inter-alpha trypsin inhibitor, heavy chain 3 + 100003_at RYR1 ryanodine receptor 1, skeletal muscle + + MG_U74Bv2.chip + Probe Set ID Gene Symbol Gene Title + 104769_at LIMA1 LIM domain and actin binding 1 + 104770_at --- 16 days neonate heart cDNA, RIKEN full-length enriched library, clone:D830033B01 product:unclassifiable, full insert sequence + 104771_at RAC2 RAS-related C3 botulinum substrate 2 + + MG_U74Cv2.chip + Probe Set ID Gene Symbol Gene Title + 128520_at CCDC97 coiled-coil domain containing 97 + 128523_at A730063M14RIK RIKEN cDNA A730063M14 gene + 128529_at A930009G19RIK RIKEN cDNA A930009G19 gene + + MOE430A.chip + Probe Set ID Gene Symbol Gene Title + 1415670_at COPG coatomer protein complex, subunit gamma + 1415671_at ATP6V0D1 ATPase, H+ transporting, lysosomal V0 subunit D1 + 1415672_at GOLGA7 golgi autoantigen, golgin subfamily a, 7 + + MOE430B.chip + Probe Set ID Gene Symbol Gene Title + 1415670_at COPG coatomer protein complex, subunit gamma + 1415671_at ATP6V0D1 ATPase, H+ transporting, lysosomal V0 subunit D1 + 1415672_at GOLGA7 golgi autoantigen, golgin subfamily a, 7 + + Mouse430_2.chip + Probe Set ID Gene Symbol Gene Title + 1415670_at COPG coatomer protein complex, subunit gamma + 1415671_at ATP6V0D1 ATPase, H+ transporting, lysosomal V0 subunit D1 + 1415672_at GOLGA7 golgi autoantigen, golgin subfamily a, 7 + + Mouse430A_2.chip + Probe Set ID Gene Symbol Gene Title + 1415670_at COPG coatomer protein complex, subunit gamma + 1415671_at ATP6V0D1 ATPase, H+ transporting, lysosomal V0 subunit D1 + 1415672_at GOLGA7 golgi autoantigen, golgin subfamily a, 7 + + Mu11KsubA.chip + Probe Set ID Gene Symbol Gene Title + aa000148_s_at NIP7 nuclear import 7 homolog (S. cerevisiae) + AA000151_at 1200011I18RIK RIKEN cDNA 1200011I18 gene + aa000380_s_at TARDBP TAR DNA binding protein + + Mu11KsubB.chip + Probe Set ID Gene Symbol Gene Title + AFFX-18SRNAMur/X00686_3_at --- --- + AFFX-18SRNAMur/X00686_5_at --- --- + AFFX-18SRNAMur/X00686_M_at --- --- + + Mu19KsubA.chip + Probe Set ID Gene Symbol Gene Title + AFFX-18SRNAMur/X00686_3_at --- --- + AFFX-18SRNAMur/X00686_5_at --- --- + AFFX-18SRNAMur/X00686_M_at --- --- + + Mu19KsubB.chip + Probe Set ID Gene Symbol Gene Title + AFFX-18SRNAMur/X00686_3_at --- --- + AFFX-18SRNAMur/X00686_5_at --- --- + AFFX-18SRNAMur/X00686_M_at --- --- + + Mu19KsubC.chip + Probe Set ID Gene Symbol Gene Title + AFFX-18SRNAMur/X00686_3_at --- --- + AFFX-18SRNAMur/X00686_5_at --- --- + AFFX-18SRNAMur/X00686_M_at --- --- + + MWG_Human_30K_A.chip + Probe Set ID Gene Symbol Gene Title + 1-A1 IFNA8 interferon, alpha 8 + 1-A10 AGL amylo-1, 6-glucosidase, 4-alpha-glucanotransferase (glycogen debranching enzyme, glycogen storage disease type III) + 1-A11 NULL NULL + + MWG_Human_30K_B.chip + Probe Set ID Gene Symbol Gene Title + 1-A10 ADAM11 a disintegrin and metalloproteinase domain 11 + 1-A11 NULL NULL + 1-A12 MAST3 microtubule associated serine/threonine kinase 3 + + Netherland_cancer_institute_operon_human_35k.chip + Probe Set ID Gene Symbol Gene Title + H200001046 ZZZ3 zinc finger, ZZ domain containing 3 [Homo sapiens]. [Source:RefSeq;Acc:NM_015534] + H200011098 ZZEF1 zinc finger, ZZ-type with EF hand domain 1 [Homo sapiens]. [Source:RefSeq;Acc:NM_015113] + H200006223 ZYX Zyxin (Zyxin 2). [Source:Uniprot/SWISSPROT;Acc:Q15942] + + Netherland_cancer_institute_operon_mouse_FOOk.chip + Probe Set ID Gene Symbol Gene Title + M300012631 ZZEF1 NULL + M300012632 ZZEF1 NULL + M200002019 ZYX Zyxin. [Source:Uniprot/SWISSPROT;Acc:Q62523] + + NIA15k.chip + Probe Set ID Gene Symbol Gene Title + H3051B03 BG067146 H3051B03-3 NIA Mouse 15K cDNA Clone Set Mus musculus cDNA + H3067H02 BG068648 H3067H02-3 NIA Mouse 15K cDNA Clone Set Mus musculus cDNA + H3121E03 AK029878 NULL + + OPERON_HUMANv2.chip + Probe Set ID Gene Symbol Gene Title + 1-A01 NULL NULL + 1-A02 NULL NULL + 1-A03 NAT2 N-acetyltransferase 2 (arylamine N-acetyltransferase) + + OPERON_HUMANv3.chip + Probe Set ID Gene Symbol Gene Title + 1-A03 TSPAN6 tetraspanin 6 + 1-A04 AK2 adenylate kinase 2 + 1-A05 NULL NULL + + RAE230A.chip + Probe Set ID Gene Symbol Gene Title + 1367452_at SUMO2 SMT3 suppressor of mif two 3 homolog 2 (yeast) + 1367453_at CDC37 cell division cycle 37 homolog (S. cerevisiae) + 1367454_at COPB2 coatomer protein complex, subunit beta 2 (beta prime) + + RAE230B.chip + Probe Set ID Gene Symbol Gene Title + 1367452_at SUMO2 SMT3 suppressor of mif two 3 homolog 2 (yeast) + 1367453_at CDC37 cell division cycle 37 homolog (S. cerevisiae) + 1367454_at COPB2 coatomer protein complex, subunit beta 2 (beta prime) + + Rat230_2.chip + Probe Set ID Gene Symbol Gene Title + 1367452_at SUMO2 SMT3 suppressor of mif two 3 homolog 2 (yeast) + 1367453_at CDC37 cell division cycle 37 homolog (S. cerevisiae) + 1367454_at COPB2 coatomer protein complex, subunit beta 2 (beta prime) + + RefSeq_human.chip + Probe Set ID Gene Symbol Gene Title + NM_030625 CXXC6 CXXC finger 6 + NM_181776 SLC36A2 solute carrier family 36 (proton/amino acid symporter), member 2 + NM_152616 TRIM42 tripartite motif-containing 42 + + RefSeq_NP_Human.chip + Probe Set ID Gene Symbol Gene Title + NP_000005 A2M alpha-2-macroglobulin + NP_000006 NAT2 N-acetyltransferase 2 (arylamine N-acetyltransferase) + NP_000007 ACADM acyl-Coenzyme A dehydrogenase, C-4 to C-12 straight chain + + RefSeq_NP_Mouse.chip + Probe Set ID Gene Symbol Gene Title + AAF62769 NULL NULL + AAF62770 NULL NULL + AAF62771 NULL NULL + + RefSeq_NP_Rat.chip + Probe Set ID Gene Symbol Gene Title + NP_007225 NULL NULL + NP_007226 NULL NULL + NP_007227 NULL NULL + + Research_Genetics.chip + Probe Set ID Gene Symbol Gene Title + 1-a-1 NULL NULL + 1-a-10 WNT2 wingless-type MMTV integration site family member 2 + 1-a-11 VHL von Hippel-Lindau tumor suppressor + + RG_U34A.chip + Probe Set ID Gene Symbol Gene Title + A01157cds_s_at LIPF lipase, gastric + A03913cds_s_at SERPINE2 serine (or cysteine) proteinase inhibitor, clade E, member 2 + A04674cds_s_at UCP1 uncoupling protein 1 (mitochondrial, proton carrier) + + RG_U34B.chip + Probe Set ID Gene Symbol Gene Title + AFFX-BioB-3_at --- --- + AFFX-BioB-3_st --- --- + AFFX-BioB-5_at --- --- + + RG_U34C.chip + Probe Set ID Gene Symbol Gene Title + AA012646_i_at --- Transcribed locus + AA012646_r_at --- Transcribed locus + AA012654_at --- Transcribed locus + + RN_U34.chip + Probe Set ID Gene Symbol Gene Title + A03913cds_s_at SERPINE2 serine (or cysteine) proteinase inhibitor, clade E, member 2 + A17753cds_s_at DRD3 dopamine receptor D3 + AA848563_s_at HSPA1A /// HSPA1B_MAPPED heat shock 70kD protein 1A /// heat shock 70kD protein 1B (mapped) + + Rosetta50K.chip + Probe Set ID Gene Symbol Gene Title + 1360465 RANBP9 RAN binding protein 9 + 1176829 LOC375449 similar to microtubule associated testis specific serine/threonine protein kinase + 1351074 NEDD4L neural precursor cell expressed, developmentally down-regulated 4-like + + Rosetta.chip + Probe Set ID Gene Symbol Gene Title + NM_000504 F10 coagulation factor X + Contig32955_RC ARL6IP6 ADP-ribosylation-like factor 6 interacting protein 6 + AK000455 MGC16733 hypothetical gene MGC16733 similar to CG12113 + + RT_U34.chip + Probe Set ID Gene Symbol Gene Title + AA108277_at HSPH1 heat shock 105kDa/110kDa protein 1 + AA108308_i_at MDM2_PREDICTED Transformed mouse 3T3 cell double minute 2 homolog (mouse) (predicted) + AA108308_s_at --- --- + + RZPD_Human_Ensembl1.1.chip + Probe Set ID Gene Symbol Gene Title + RZPDp203A011001D SARDH sarcosine dehydrogenase + RZPDp203A011002D ARHGAP22 Rho GTPase activating protein 22 + RZPDp203A011003D CNGA3 cyclic nucleotide gated channel alpha 3 + + RZPD_Human_ORF_Clones_Gateway.chip + Probe Set ID Gene Symbol Gene Title + RZPDo834A0110D - Gateway (closed) PTD015 PTD015 protein + RZPDo834A0114D - Gateway (closed) TRIB3 tribbles homolog 3 (Drosophila) + RZPDo834A0116D - Gateway (closed) ORM2 orosomucoid 2 + + RZPD_Human_Unigene3.1.chip + Probe Set ID Gene Symbol Gene Title + HU3_p983A011001D SARDH sarcosine dehydrogenase + HU3_p983A011002D ARHGAP22 Rho GTPase activating protein 22 + HU3_p983A011003D CNGA3 cyclic nucleotide gated channel alpha 3 + + Seq_Accession.chip + Probe Set ID Gene Symbol + AA017197 C21ORF36 + AA191116 MTVR2 + AA280701 CXYORF7 + + Stanford.chip + Probe Set ID Gene Symbol Gene Title + IMAGE:703849 DDB2 damage-specific DNA binding protein 2, 48kDa + IMAGE:1301778 ZFY zinc finger protein, Y-linked + IMAGE:795810 HS.99503HS.520681 Homo sapiens transcribed sequenceHomo sapiens, clone IMAGE:4823270, mRNA + + Stanford_Source_Accessions.chip + Probe Set ID Gene Symbol Gene Title + AI848107 0610010K14RIK RIKEN cDNA 0610010K14 gene + AK002491 0610010K14RIK RIKEN cDNA 0610010K14 gene + AK003842 0610010K14RIK RIKEN cDNA 0610010K14 gene + + TIGR_31K_Human_Set.chip + Probe Set ID Gene Symbol Gene Title + 1-1 NULL NULL + 1-10 WNT2 wingless-type MMTV integration site family member 2 + 1-11 VHL von Hippel-Lindau tumor suppressor + + TIGR_40K_Human_Set.chip + Probe Set ID Gene Symbol Gene Title + 10 NULL NULL + 100 TEX27 testis expressed sequence 27 + 1000 HOXA1 homeo box A1 + + U133_X3P.chip + Probe Set ID Gene Symbol Gene Title + 1053_3p_at RFC2 replication factor C (activator 1) 2, 40kDa + 117_3p_at HSPA6 /// LOC652878 heat shock 70kDa protein 6 (HSP70B') /// similar to heat shock 70kDa protein 6 (HSP70B) + 1494_3p_f_at CYP2A6 cytochrome P450, family 2, subfamily A, polypeptide 6 + + UCLA_NIH_33K.chip + Probe Set ID Gene Symbol Gene Title + 1020181 NULL NULL + 1020315 VAV2 vav 2 oncogene + 1020478 AP1GBP1 AP1 gamma subunit binding protein 1 + + Zebrafish.chip + Probe Set ID Gene Symbol Gene Title + AFFX-BioB-3_at --- --- + AFFX-BioB-5_at --- --- + AFFX-BioB-M_at --- --- + + + .. _LGPL: http://www.gnu.org/copyleft/lesser.html + .. _GSEA: http://www.broadinstitute.org/gsea + .. _GUIDE: http://www.broadinstitute.org/gsea/doc/GSEAUserGuideFrame.html?_Interpreting_GSEA_Results + .. _MSigDB: http://www.broadinstitute.org/gsea/msigdb/index.jsp + .. _2005Paper: http://www.pnas.org/content/102/43/15545.full + +</help> + +</tool> + +