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_mergedClustering1.methlyationcnmf	BLCA-TP.bestclus.txt	gdac.broadinstitute.org_BLCA-TP.Methylation_Clustering_CNMF.Level_4.2013042100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00255:23	Aggregate_Molecular_Subtype_Clusters_2013042100	BLCA-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_BLCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013042100.0.0	yes
GDAC_mergedClustering1.methlyationcnmf	BLCA-TP.bestclus.txt	gdac.broadinstitute.org_BLCA-TP.Methylation_Clustering_CNMF.Level_4.2013042100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00255:23	Aggregate_Molecular_Subtype_Clusters_2013042100	report.html	report	Level_4	html	gdac.broadinstitute.org_BLCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013042100.0.0	yes
GDAC_mergedClustering1.miRseqhc	BLCA-TP.bestclus.txt	gdac.broadinstitute.org_BLCA-TP.miRseq_Clustering_Consensus.Level_4.2013042100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00255:23	Aggregate_Molecular_Subtype_Clusters_2013042100	BLCA-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_BLCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013042100.0.0	yes
GDAC_mergedClustering1.miRseqhc	BLCA-TP.bestclus.txt	gdac.broadinstitute.org_BLCA-TP.miRseq_Clustering_Consensus.Level_4.2013042100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00255:23	Aggregate_Molecular_Subtype_Clusters_2013042100	report.html	report	Level_4	html	gdac.broadinstitute.org_BLCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013042100.0.0	yes
GDAC_mergedClustering1.miRseqcnmf	BLCA-TP.bestclus.txt	gdac.broadinstitute.org_BLCA-TP.miRseq_Clustering_CNMF.Level_4.2013042100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00255:23	Aggregate_Molecular_Subtype_Clusters_2013042100	BLCA-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_BLCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013042100.0.0	yes
GDAC_mergedClustering1.miRseqcnmf	BLCA-TP.bestclus.txt	gdac.broadinstitute.org_BLCA-TP.miRseq_Clustering_CNMF.Level_4.2013042100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00255:23	Aggregate_Molecular_Subtype_Clusters_2013042100	report.html	report	Level_4	html	gdac.broadinstitute.org_BLCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013042100.0.0	yes
GDAC_mergedClustering1.mRNAseqcnmf	BLCA-TP.bestclus.txt	gdac.broadinstitute.org_BLCA-TP.mRNAseq_Clustering_CNMF.Level_4.2013042100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00255:23	Aggregate_Molecular_Subtype_Clusters_2013042100	BLCA-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_BLCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013042100.0.0	yes
GDAC_mergedClustering1.mRNAseqcnmf	BLCA-TP.bestclus.txt	gdac.broadinstitute.org_BLCA-TP.mRNAseq_Clustering_CNMF.Level_4.2013042100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00255:23	Aggregate_Molecular_Subtype_Clusters_2013042100	report.html	report	Level_4	html	gdac.broadinstitute.org_BLCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013042100.0.0	yes
GDAC_mergedClustering1.PredictionU133aPhilips	BLCA-TP.bestclus.txt	gdac.broadinstitute.org_BLCA-TP.RPPA_Clustering_Consensus.Level_4.2013042100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00255:23	Aggregate_Molecular_Subtype_Clusters_2013042100	BLCA-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_BLCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013042100.0.0	yes
GDAC_mergedClustering1.PredictionU133aPhilips	BLCA-TP.bestclus.txt	gdac.broadinstitute.org_BLCA-TP.RPPA_Clustering_Consensus.Level_4.2013042100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00255:23	Aggregate_Molecular_Subtype_Clusters_2013042100	report.html	report	Level_4	html	gdac.broadinstitute.org_BLCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013042100.0.0	yes
GDAC_mergedClustering1.PredictionU133aTCGA	BLCA-TP.bestclus.txt	gdac.broadinstitute.org_BLCA-TP.RPPA_Clustering_CNMF.Level_4.2013042100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00255:23	Aggregate_Molecular_Subtype_Clusters_2013042100	BLCA-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_BLCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013042100.0.0	yes
GDAC_mergedClustering1.PredictionU133aTCGA	BLCA-TP.bestclus.txt	gdac.broadinstitute.org_BLCA-TP.RPPA_Clustering_CNMF.Level_4.2013042100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00255:23	Aggregate_Molecular_Subtype_Clusters_2013042100	report.html	report	Level_4	html	gdac.broadinstitute.org_BLCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013042100.0.0	yes
GDAC_mergedClustering1.mRNAseqhc	BLCA-TP.bestclus.txt	gdac.broadinstitute.org_BLCA-TP.mRNAseq_Clustering_Consensus.Level_4.2013042100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00255:23	Aggregate_Molecular_Subtype_Clusters_2013042100	BLCA-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_BLCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013042100.0.0	yes
GDAC_mergedClustering1.mRNAseqhc	BLCA-TP.bestclus.txt	gdac.broadinstitute.org_BLCA-TP.mRNAseq_Clustering_Consensus.Level_4.2013042100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00255:23	Aggregate_Molecular_Subtype_Clusters_2013042100	report.html	report	Level_4	html	gdac.broadinstitute.org_BLCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013042100.0.0	yes
GDAC_mergedClustering1.copynumber	BLCA-TP.bestclus.txt	gdac.broadinstitute.org_BLCA-TP.CopyNumber_Clustering_CNMF.Level_4.2013042100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00255:23	Aggregate_Molecular_Subtype_Clusters_2013042100	BLCA-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_BLCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013042100.0.0	yes
GDAC_mergedClustering1.copynumber	BLCA-TP.bestclus.txt	gdac.broadinstitute.org_BLCA-TP.CopyNumber_Clustering_CNMF.Level_4.2013042100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00255:23	Aggregate_Molecular_Subtype_Clusters_2013042100	report.html	report	Level_4	html	gdac.broadinstitute.org_BLCA-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2013042100.0.0	yes
