Pipeline Input Name	Archive Result File REF	Comment [TCGA Archive Name]	Protocol REF	Data Transformation Name	Derived Data File	Comment [TCGA Data Type]	Comment [TCGA Data Level]	Comment [TCGA File Type]	Comment [TCGA Archive Name]	Comment [TCGA Include for Analysis]
GDAC_geneListPathwayEnrichment:refseqGeneInfo	hg18_refseq_download.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	pwEnrich_marker_subtype1.txt	Genes_subptyeClassifer_exprCghCor	Level_4	text	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:refseqGeneInfo	hg18_refseq_download.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	pwEnrich_marker_subtype2.txt	Genes_subptyeClassifer_exprCghCor	Level_4	text	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:refseqGeneInfo	hg18_refseq_download.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	pwEnrich_marker_subtype3.txt	Genes_subptyeClassifer_exprCghCor	Level_4	text	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:refseqGeneInfo	hg18_refseq_download.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:refseqGeneInfo	hg18_refseq_download.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:geneList_gisticDel	del_genes.conf_99.txt	gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	pwEnrich_marker_subtype1.txt	Genes_subptyeClassifer_exprCghCor	Level_4	text	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:geneList_gisticDel	del_genes.conf_99.txt	gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	pwEnrich_marker_subtype2.txt	Genes_subptyeClassifer_exprCghCor	Level_4	text	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:geneList_gisticDel	del_genes.conf_99.txt	gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	pwEnrich_marker_subtype3.txt	Genes_subptyeClassifer_exprCghCor	Level_4	text	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:geneList_gisticDel	del_genes.conf_99.txt	gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:geneList_gisticDel	del_genes.conf_99.txt	gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:geneList_mutation	sig_genes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	pwEnrich_marker_subtype1.txt	Genes_subptyeClassifer_exprCghCor	Level_4	text	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:geneList_mutation	sig_genes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	pwEnrich_marker_subtype2.txt	Genes_subptyeClassifer_exprCghCor	Level_4	text	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:geneList_mutation	sig_genes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	pwEnrich_marker_subtype3.txt	Genes_subptyeClassifer_exprCghCor	Level_4	text	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:geneList_mutation	sig_genes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:geneList_mutation	sig_genes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:geneList_expr	UCEC-TP.subclassmarkers.txt	gdac.broadinstitute.org_UCEC-TP.mRNAseq_Clustering_Consensus_Plus.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	pwEnrich_marker_subtype1.txt	Genes_subptyeClassifer_exprCghCor	Level_4	text	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:geneList_expr	UCEC-TP.subclassmarkers.txt	gdac.broadinstitute.org_UCEC-TP.mRNAseq_Clustering_Consensus_Plus.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	pwEnrich_marker_subtype2.txt	Genes_subptyeClassifer_exprCghCor	Level_4	text	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:geneList_expr	UCEC-TP.subclassmarkers.txt	gdac.broadinstitute.org_UCEC-TP.mRNAseq_Clustering_Consensus_Plus.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	pwEnrich_marker_subtype3.txt	Genes_subptyeClassifer_exprCghCor	Level_4	text	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:geneList_expr	UCEC-TP.subclassmarkers.txt	gdac.broadinstitute.org_UCEC-TP.mRNAseq_Clustering_Consensus_Plus.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:geneList_expr	UCEC-TP.subclassmarkers.txt	gdac.broadinstitute.org_UCEC-TP.mRNAseq_Clustering_Consensus_Plus.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:MSigDB_C2	c2.cp.v3.0-2.symbols.gmt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	pwEnrich_marker_subtype1.txt	Genes_subptyeClassifer_exprCghCor	Level_4	text	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:MSigDB_C2	c2.cp.v3.0-2.symbols.gmt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	pwEnrich_marker_subtype2.txt	Genes_subptyeClassifer_exprCghCor	Level_4	text	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:MSigDB_C2	c2.cp.v3.0-2.symbols.gmt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	pwEnrich_marker_subtype3.txt	Genes_subptyeClassifer_exprCghCor	Level_4	text	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:MSigDB_C2	c2.cp.v3.0-2.symbols.gmt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:MSigDB_C2	c2.cp.v3.0-2.symbols.gmt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:geneList_exprCghCor	UCEC-TP.CORS.tsv	gdac.broadinstitute.org_UCEC-TP.Correlate_CopyNumber_vs_mRNA.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	pwEnrich_marker_subtype1.txt	Genes_subptyeClassifer_exprCghCor	Level_4	text	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:geneList_exprCghCor	UCEC-TP.CORS.tsv	gdac.broadinstitute.org_UCEC-TP.Correlate_CopyNumber_vs_mRNA.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	pwEnrich_marker_subtype2.txt	Genes_subptyeClassifer_exprCghCor	Level_4	text	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:geneList_exprCghCor	UCEC-TP.CORS.tsv	gdac.broadinstitute.org_UCEC-TP.Correlate_CopyNumber_vs_mRNA.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	pwEnrich_marker_subtype3.txt	Genes_subptyeClassifer_exprCghCor	Level_4	text	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:geneList_exprCghCor	UCEC-TP.CORS.tsv	gdac.broadinstitute.org_UCEC-TP.Correlate_CopyNumber_vs_mRNA.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:geneList_exprCghCor	UCEC-TP.CORS.tsv	gdac.broadinstitute.org_UCEC-TP.Correlate_CopyNumber_vs_mRNA.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:geneList_gisticAmp	amp_genes.conf_99.txt	gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	pwEnrich_marker_subtype1.txt	Genes_subptyeClassifer_exprCghCor	Level_4	text	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:geneList_gisticAmp	amp_genes.conf_99.txt	gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	pwEnrich_marker_subtype2.txt	Genes_subptyeClassifer_exprCghCor	Level_4	text	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:geneList_gisticAmp	amp_genes.conf_99.txt	gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	pwEnrich_marker_subtype3.txt	Genes_subptyeClassifer_exprCghCor	Level_4	text	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:geneList_gisticAmp	amp_genes.conf_99.txt	gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
GDAC_geneListPathwayEnrichment:geneList_gisticAmp	amp_genes.conf_99.txt	gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.Level_4.2014101700.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00291:39	Pathway_FindEnrichedGenes_2014101700	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_UCEC-TP.Pathway_FindEnrichedGenes.Level_4.2014101700.0.0	yes
