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/LUSC-TP/2662146/3.GDAC_selectBestcluster.Finished/LUSC-TP.subclassmarkers.txt |
GDAC_geneListPathwayEnrichment1 geneList_gisticAmp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/LUSC-TP/2662124/amp_genes.conf_99.txt |
GDAC_geneListPathwayEnrichment1 geneList_gisticDel | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/LUSC-TP/2662124/del_genes.conf_99.txt |
GDAC_geneListPathwayEnrichment1 geneList_exprCghCor | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/getCopyNumberExpCor/LUSC-TP/2663979/1.getCNExpCorrelation.Finished/LUSC-TP.CORS.tsv |
GDAC_geneListPathwayEnrichment1 geneList_mutation | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/LUSC-TP/2662451/LUSC-TP.sig_genes.txt |
GDAC_geneListPathwayEnrichment1 outPrefix | pathwayEnrich |
Execution Times: | |
Submitted: | 07:26:39 05-03-13 |
Completed: | |
Elapsed: | 00 hrs 01 mins 36 secs |
step 1. GDAC_geneListPathwayEnrichment [id: 335995] 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/LUSC-TP/2662146/3.GDAC_selectBestcluster.Finished/LUSC-TP.subclassmarkers.txt |
geneList_gisticAmp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/LUSC-TP/2662124/amp_genes.conf_99.txt |
geneList_gisticDel | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/LUSC-TP/2662124/del_genes.conf_99.txt |
geneList_exprCghCor | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/getCopyNumberExpCor/LUSC-TP/2663979/1.getCNExpCorrelation.Finished/LUSC-TP.CORS.tsv |
geneList_mutation | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/LUSC-TP/2662451/LUSC-TP.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: | 07:26:42 05-03-13 |
Completed: | 07:28:01 05-03-13 |
Elapsed: | 00 hrs 01 mins 19 secs |
step 2. GDAC_geneListPathwayEnrichmentReport [id: 335997] 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: | |
pwEnrich_marker_subtype1.txt | |
pwEnrich_marker_subtype2.txt | |
pwEnrich_marker_subtype3.txt | |
nozzle.RData | |
nozzle.html | |
.lsf.out | |
stdout.txt |
Execution Times: | |
Submitted: | 07:26:42 05-03-13 |
Completed: | 07:28:14 05-03-13 |
Elapsed: | 00 hrs 01 mins 32 secs |