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]
ClinicalAnalysisAllGenes_new:clinical.file.name	BRCA-TP.merged_data.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:140	Correlate_Clinical_vs_RPPA_2015082100	table1.txt	clinical_Correlation-Clinical_Expression	Level_4	text	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_RPPA.Level_4.2015082100.0.0	yes
ClinicalAnalysisAllGenes_new:clinical.file.name	BRCA-TP.merged_data.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:140	Correlate_Clinical_vs_RPPA_2015082100	supp.table1.txt	clinical_Correlation-Clinical_Expression	Level_4	text	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_RPPA.Level_4.2015082100.0.0	yes
ClinicalAnalysisAllGenes_new:clinical.file.name	BRCA-TP.merged_data.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:140	Correlate_Clinical_vs_RPPA_2015082100	excluded_gender_correlated_genes_located_in_SexChromosomes.txt	clinical_Correlation-Clinical_Expression	Level_4	text	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_RPPA.Level_4.2015082100.0.0	yes
ClinicalAnalysisAllGenes_new:data.file.name	BRCA-TP.rppa.txt	gdac.broadinstitute.org_BRCA-TP.RPPA_AnnotateWithGene.Level_3.2015082100.2.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:140	Correlate_Clinical_vs_RPPA_2015082100	table1.txt	clinical_Correlation-Clinical_Expression	Level_4	text	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_RPPA.Level_4.2015082100.0.0	yes
ClinicalAnalysisAllGenes_new:data.file.name	BRCA-TP.rppa.txt	gdac.broadinstitute.org_BRCA-TP.RPPA_AnnotateWithGene.Level_3.2015082100.2.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:140	Correlate_Clinical_vs_RPPA_2015082100	supp.table1.txt	clinical_Correlation-Clinical_Expression	Level_4	text	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_RPPA.Level_4.2015082100.0.0	yes
ClinicalAnalysisAllGenes_new:data.file.name	BRCA-TP.rppa.txt	gdac.broadinstitute.org_BRCA-TP.RPPA_AnnotateWithGene.Level_3.2015082100.2.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:140	Correlate_Clinical_vs_RPPA_2015082100	excluded_gender_correlated_genes_located_in_SexChromosomes.txt	clinical_Correlation-Clinical_Expression	Level_4	text	gdac.broadinstitute.org_BRCA-TP.Correlate_Clinical_vs_RPPA.Level_4.2015082100.0.0	yes
