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]
Correlate_Clinical_Clusters_onlysig2.clinical.info.file	BRCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_BRCA-TP.Clinical_Pick_Tier1.Level_4.2013092300.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	BRCA-TP.mutsig.cluster.txt	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	txt	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
Correlate_Clinical_Clusters_onlysig2.clinical.info.file	BRCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_BRCA-TP.Clinical_Pick_Tier1.Level_4.2013092300.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	table.1.txt	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	txt	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
Correlate_Clinical_Clusters_onlysig2.clinical.info.file	BRCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_BRCA-TP.Clinical_Pick_Tier1.Level_4.2013092300.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	D19V8.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
Correlate_Clinical_Clusters_onlysig2.clinical.info.file	BRCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_BRCA-TP.Clinical_Pick_Tier1.Level_4.2013092300.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	D24V10.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
Correlate_Clinical_Clusters_onlysig2.clinical.info.file	BRCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_BRCA-TP.Clinical_Pick_Tier1.Level_4.2013092300.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	D89V10.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
Correlate_Clinical_Clusters_onlysig2.clinical.info.file	BRCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_BRCA-TP.Clinical_Pick_Tier1.Level_4.2013092300.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	D53V8.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
Correlate_Clinical_Clusters_onlysig2.clinical.info.file	BRCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_BRCA-TP.Clinical_Pick_Tier1.Level_4.2013092300.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	D16V2.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
Correlate_Clinical_Clusters_onlysig2.clinical.info.file	BRCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_BRCA-TP.Clinical_Pick_Tier1.Level_4.2013092300.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	D5V10.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
Correlate_Clinical_Clusters_onlysig2.clinical.info.file	BRCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_BRCA-TP.Clinical_Pick_Tier1.Level_4.2013092300.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	D81V3.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
Correlate_Clinical_Clusters_onlysig2.clinical.info.file	BRCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_BRCA-TP.Clinical_Pick_Tier1.Level_4.2013092300.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	D56V8.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
Correlate_Clinical_Clusters_onlysig2.clinical.info.file	BRCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_BRCA-TP.Clinical_Pick_Tier1.Level_4.2013092300.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	D21V8.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
Correlate_Clinical_Clusters_onlysig2.clinical.info.file	BRCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_BRCA-TP.Clinical_Pick_Tier1.Level_4.2013092300.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	D29V3.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
Correlate_Clinical_Clusters_onlysig2.clinical.info.file	BRCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_BRCA-TP.Clinical_Pick_Tier1.Level_4.2013092300.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	D68V8.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
Correlate_Clinical_Clusters_onlysig2.clinical.info.file	BRCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_BRCA-TP.Clinical_Pick_Tier1.Level_4.2013092300.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	D50V10.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
Correlate_Clinical_Clusters_onlysig2.clinical.info.file	BRCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_BRCA-TP.Clinical_Pick_Tier1.Level_4.2013092300.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	D72V10.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
Correlate_Clinical_Clusters_onlysig2.clinical.info.file	BRCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_BRCA-TP.Clinical_Pick_Tier1.Level_4.2013092300.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
Correlate_Clinical_Clusters_onlysig2.clinical.info.file	BRCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_BRCA-TP.Clinical_Pick_Tier1.Level_4.2013092300.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
mutsig2cluster_new1.sample.gene.table.file	BRCA-TP.sample_sig_gene_table.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	BRCA-TP.mutsig.cluster.txt	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	txt	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
mutsig2cluster_new1.sample.gene.table.file	BRCA-TP.sample_sig_gene_table.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	table.1.txt	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	txt	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
mutsig2cluster_new1.sample.gene.table.file	BRCA-TP.sample_sig_gene_table.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	D19V8.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
mutsig2cluster_new1.sample.gene.table.file	BRCA-TP.sample_sig_gene_table.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	D24V10.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
mutsig2cluster_new1.sample.gene.table.file	BRCA-TP.sample_sig_gene_table.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	D89V10.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
mutsig2cluster_new1.sample.gene.table.file	BRCA-TP.sample_sig_gene_table.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	D53V8.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
mutsig2cluster_new1.sample.gene.table.file	BRCA-TP.sample_sig_gene_table.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	D16V2.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
mutsig2cluster_new1.sample.gene.table.file	BRCA-TP.sample_sig_gene_table.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	D5V10.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
mutsig2cluster_new1.sample.gene.table.file	BRCA-TP.sample_sig_gene_table.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	D81V3.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
mutsig2cluster_new1.sample.gene.table.file	BRCA-TP.sample_sig_gene_table.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	D56V8.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
mutsig2cluster_new1.sample.gene.table.file	BRCA-TP.sample_sig_gene_table.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	D21V8.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
mutsig2cluster_new1.sample.gene.table.file	BRCA-TP.sample_sig_gene_table.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	D29V3.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
mutsig2cluster_new1.sample.gene.table.file	BRCA-TP.sample_sig_gene_table.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	D68V8.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
mutsig2cluster_new1.sample.gene.table.file	BRCA-TP.sample_sig_gene_table.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	D50V10.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
mutsig2cluster_new1.sample.gene.table.file	BRCA-TP.sample_sig_gene_table.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	D72V10.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
mutsig2cluster_new1.sample.gene.table.file	BRCA-TP.sample_sig_gene_table.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
mutsig2cluster_new1.sample.gene.table.file	BRCA-TP.sample_sig_gene_table.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00339:23	Correlate_Clinical_vs_Mutation_2013092300	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_Mutation.Level_4.2013092300.0.0	yes
