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]
miRseqMaturecnmf	CHOL-TP.bestclus.txt	gdac.broadinstitute.org_CHOL-TP.miRseq_Mature_Clustering_CNMF.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2016012800	CHOL-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_CHOL-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2016012800.0.0	yes
PredictionU133aPhilips	CHOL-TP.bestclus.txt	gdac.broadinstitute.org_CHOL-TP.RPPA_Clustering_Consensus_Plus.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2016012800	CHOL-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_CHOL-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2016012800.0.0	yes
methylationcnmf	CHOL-TP.bestclus.txt	gdac.broadinstitute.org_CHOL-TP.Methylation_Clustering_CNMF.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2016012800	CHOL-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_CHOL-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2016012800.0.0	yes
mRNAseqcnmf	CHOL-TP.bestclus.txt	gdac.broadinstitute.org_CHOL-TP.mRNAseq_Clustering_CNMF.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2016012800	CHOL-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_CHOL-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2016012800.0.0	yes
miRseqcnmf	CHOL-TP.bestclus.txt	gdac.broadinstitute.org_CHOL-TP.miRseq_Clustering_CNMF.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2016012800	CHOL-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_CHOL-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2016012800.0.0	yes
mRNAseqhc	CHOL-TP.bestclus.txt	gdac.broadinstitute.org_CHOL-TP.mRNAseq_Clustering_Consensus_Plus.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2016012800	CHOL-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_CHOL-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2016012800.0.0	yes
miRseqhc	CHOL-TP.bestclus.txt	gdac.broadinstitute.org_CHOL-TP.miRseq_Clustering_Consensus_Plus.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2016012800	CHOL-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_CHOL-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2016012800.0.0	yes
PredictionU133aTCGA	CHOL-TP.bestclus.txt	gdac.broadinstitute.org_CHOL-TP.RPPA_Clustering_CNMF.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2016012800	CHOL-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_CHOL-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2016012800.0.0	yes
miRseqMaturehc	CHOL-TP.bestclus.txt	gdac.broadinstitute.org_CHOL-TP.miRseq_Mature_Clustering_Consensus_Plus.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2016012800	CHOL-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_CHOL-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2016012800.0.0	yes
copynumber	CHOL-TP.bestclus.txt	gdac.broadinstitute.org_CHOL-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:2	Aggregate_Molecular_Subtype_Clusters_2016012800	CHOL-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_CHOL-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2016012800.0.0	yes
