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]
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_CESC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	table.1.txt	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	txt	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_CESC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D23V4.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_CESC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D13V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_CESC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D19V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_CESC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D27V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_CESC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D43V4.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_CESC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D43V2.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_CESC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D4V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_CESC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D28V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_CESC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D21V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_CESC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D26V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_CESC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D30V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_CESC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D5V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_CESC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D3V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_CESC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D40V4.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_CESC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D37V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_CESC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_CESC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
Correlate_Cluster_cnvs_onlysig2.clinical.info.file	CESC-TP.transferedmergedcluster.txt	gdac.broadinstitute.org_CESC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	table.1.txt	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	txt	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
Correlate_Cluster_cnvs_onlysig2.clinical.info.file	CESC-TP.transferedmergedcluster.txt	gdac.broadinstitute.org_CESC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D23V4.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
Correlate_Cluster_cnvs_onlysig2.clinical.info.file	CESC-TP.transferedmergedcluster.txt	gdac.broadinstitute.org_CESC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D13V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
Correlate_Cluster_cnvs_onlysig2.clinical.info.file	CESC-TP.transferedmergedcluster.txt	gdac.broadinstitute.org_CESC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D19V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
Correlate_Cluster_cnvs_onlysig2.clinical.info.file	CESC-TP.transferedmergedcluster.txt	gdac.broadinstitute.org_CESC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D27V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
Correlate_Cluster_cnvs_onlysig2.clinical.info.file	CESC-TP.transferedmergedcluster.txt	gdac.broadinstitute.org_CESC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D43V4.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
Correlate_Cluster_cnvs_onlysig2.clinical.info.file	CESC-TP.transferedmergedcluster.txt	gdac.broadinstitute.org_CESC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D43V2.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
Correlate_Cluster_cnvs_onlysig2.clinical.info.file	CESC-TP.transferedmergedcluster.txt	gdac.broadinstitute.org_CESC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D4V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
Correlate_Cluster_cnvs_onlysig2.clinical.info.file	CESC-TP.transferedmergedcluster.txt	gdac.broadinstitute.org_CESC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D28V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
Correlate_Cluster_cnvs_onlysig2.clinical.info.file	CESC-TP.transferedmergedcluster.txt	gdac.broadinstitute.org_CESC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D21V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
Correlate_Cluster_cnvs_onlysig2.clinical.info.file	CESC-TP.transferedmergedcluster.txt	gdac.broadinstitute.org_CESC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D26V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
Correlate_Cluster_cnvs_onlysig2.clinical.info.file	CESC-TP.transferedmergedcluster.txt	gdac.broadinstitute.org_CESC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D30V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
Correlate_Cluster_cnvs_onlysig2.clinical.info.file	CESC-TP.transferedmergedcluster.txt	gdac.broadinstitute.org_CESC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D5V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
Correlate_Cluster_cnvs_onlysig2.clinical.info.file	CESC-TP.transferedmergedcluster.txt	gdac.broadinstitute.org_CESC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D3V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
Correlate_Cluster_cnvs_onlysig2.clinical.info.file	CESC-TP.transferedmergedcluster.txt	gdac.broadinstitute.org_CESC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D40V4.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
Correlate_Cluster_cnvs_onlysig2.clinical.info.file	CESC-TP.transferedmergedcluster.txt	gdac.broadinstitute.org_CESC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	D37V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
Correlate_Cluster_cnvs_onlysig2.clinical.info.file	CESC-TP.transferedmergedcluster.txt	gdac.broadinstitute.org_CESC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
Correlate_Cluster_cnvs_onlysig2.clinical.info.file	CESC-TP.transferedmergedcluster.txt	gdac.broadinstitute.org_CESC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00505:4	Correlate_molecularSubtype_vs_CopyNumber_Focal_2013092300	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_CESC-TP.Correlate_molecularSubtype_vs_CopyNumber_Focal.Level_4.2013092300.0.0	yes
