| GDAC_geneListPathwayEnrichment1 MSigDB_C2 | file:/xchip/cga/reference/MSigDB/c2.cp.v3.0-2.symbols.gmt |
| GDAC_geneListPathwayEnrichment1 refseqGeneInfo | file:/xchip/cga/reference/hg18_refseq_download.txt |
| GDAC_geneListPathwayEnrichment1 geneList_expr | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_ConsensusClusteringPipeline/COAD/2008335/3.GDAC_selectBestcluster.Finished/COAD.subclassmarkers.txt |
| GDAC_geneListPathwayEnrichment1 geneList_gisticAmp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Pipeline/COAD/2018643/1.Gistic2_Analysis.Finished/amp_genes.conf_99.txt |
| GDAC_geneListPathwayEnrichment1 geneList_gisticDel | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Pipeline/COAD/2018643/1.Gistic2_Analysis.Finished/del_genes.conf_99.txt |
| GDAC_geneListPathwayEnrichment1 geneList_exprCghCor | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/getCopyNumberExpCor/COAD/2008352/1.getCNExpCorrelation.Finished/COAD.CORS.tsv |
| GDAC_geneListPathwayEnrichment1 geneList_mutation | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/COAD/1910375/0.MutSigRun.Finished/COAD.sig_genes.txt |
| GDAC_geneListPathwayEnrichment1 outPrefix | pathwayEnrich |
| Execution Times: | |
| Submitted: | 20:57:41 09-11-12 |
| Completed: | |
| Elapsed: | 00 hrs 03 mins 14 secs |
step 1. GDAC_geneListPathwayEnrichment [id: 226736] Find pathways genes enriched in a gene list
urn:lsid:broadinstitute.org:cancer.genome.analysis:00268:29
| MSigDB_C2 | file:/xchip/cga/reference/MSigDB/c2.cp.v3.0-2.symbols.gmt |
| refseqGeneInfo | file:/xchip/cga/reference/hg18_refseq_download.txt |
| geneList_expr | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_ConsensusClusteringPipeline/COAD/2008335/3.GDAC_selectBestcluster.Finished/COAD.subclassmarkers.txt |
| geneList_gisticAmp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Pipeline/COAD/2018643/1.Gistic2_Analysis.Finished/amp_genes.conf_99.txt |
| geneList_gisticDel | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Pipeline/COAD/2018643/1.Gistic2_Analysis.Finished/del_genes.conf_99.txt |
| geneList_exprCghCor | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/getCopyNumberExpCor/COAD/2008352/1.getCNExpCorrelation.Finished/COAD.CORS.tsv |
| geneList_mutation | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/COAD/1910375/0.MutSigRun.Finished/COAD.sig_genes.txt |
| outPrefix | pathwayEnrich |
| Output Files: | |
| genes_withMut.txt | |
| genes_withCNV_andHighExprCor.txt | |
| pathwayEnrich_cnvOrMut.txt | |
| .lsf.out | |
| pathwayEnrich_subclassMarker.txt | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 20:57:44 09-11-12 |
| Completed: | 21:00:29 09-11-12 |
| Elapsed: | 00 hrs 02 mins 44 secs |
step 2. GDAC_geneListPathwayEnrichmentReport [id: 226737] GeneListPathwayEnrichment Report
urn:lsid:broadinstitute.org:cancer.genome.analysis:00290:27
| pwEnrich_cnvOrMut | pathwayEnrich_cnvOrMut.txt |
| pwEnrich_subclassMarker | pathwayEnrich_subclassMarker.txt |
| genes_withMut | genes_withMut.txt |
| genes_withCNV | genes_withCNV_andHighExprCor.txt |
| Output Files: | |
| nozzle.html | |
| pwEnrich_marker_subtype1.txt | |
| pwEnrich_marker_subtype2.txt | |
| pwEnrich_marker_subtype4.txt | |
| pwEnrich_marker_subtype3.txt | |
| .lsf.out | |
| nozzle.RData | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 20:57:44 09-11-12 |
| Completed: | 21:00:54 09-11-12 |
| Elapsed: | 00 hrs 03 mins 09 secs |