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]
mRNAseqcnmf	LUSC-TP.bestclus.txt	gdac.broadinstitute.org_LUSC-TP.mRNAseq_Clustering_CNMF.Level_4.2014071500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:1	Aggregate_Molecular_Subtype_Clusters_2014071500	LUSC-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_LUSC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2014071500.0.0	yes
mrnahc	LUSC-TP.bestclus.txt	gdac.broadinstitute.org_LUSC-TP.mRNA_Clustering_Consensus_Plus.Level_4.2014071500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:1	Aggregate_Molecular_Subtype_Clusters_2014071500	LUSC-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_LUSC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2014071500.0.0	yes
miRseqMaturecnmf	LUSC-TP.bestclus.txt	gdac.broadinstitute.org_LUSC-TP.miRseq_Mature_Clustering_CNMF.Level_4.2014071500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:1	Aggregate_Molecular_Subtype_Clusters_2014071500	LUSC-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_LUSC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2014071500.0.0	yes
mrnacnmf	LUSC-TP.bestclus.txt	gdac.broadinstitute.org_LUSC-TP.mRNA_Clustering_CNMF.Level_4.2014071500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:1	Aggregate_Molecular_Subtype_Clusters_2014071500	LUSC-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_LUSC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2014071500.0.0	yes
PredictionU133aPhilips	LUSC-TP.bestclus.txt	gdac.broadinstitute.org_LUSC-TP.RPPA_Clustering_Consensus_Plus.Level_4.2014071500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:1	Aggregate_Molecular_Subtype_Clusters_2014071500	LUSC-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_LUSC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2014071500.0.0	yes
miRseqcnmf	LUSC-TP.bestclus.txt	gdac.broadinstitute.org_LUSC-TP.miRseq_Clustering_CNMF.Level_4.2014071500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:1	Aggregate_Molecular_Subtype_Clusters_2014071500	LUSC-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_LUSC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2014071500.0.0	yes
miRseqMaturehc	LUSC-TP.bestclus.txt	gdac.broadinstitute.org_LUSC-TP.miRseq_Mature_Clustering_Consensus_Plus.Level_4.2014071500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:1	Aggregate_Molecular_Subtype_Clusters_2014071500	LUSC-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_LUSC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2014071500.0.0	yes
methylationcnmf	LUSC-TP.bestclus.txt	gdac.broadinstitute.org_LUSC-TP.Methylation_Clustering_CNMF.Level_4.2014071500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:1	Aggregate_Molecular_Subtype_Clusters_2014071500	LUSC-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_LUSC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2014071500.0.0	yes
copynumber	LUSC-TP.bestclus.txt	gdac.broadinstitute.org_LUSC-TP.CopyNumber_Clustering_CNMF.Level_4.2014071500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:1	Aggregate_Molecular_Subtype_Clusters_2014071500	LUSC-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_LUSC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2014071500.0.0	yes
mRNAseqhc	LUSC-TP.bestclus.txt	gdac.broadinstitute.org_LUSC-TP.mRNAseq_Clustering_Consensus_Plus.Level_4.2014071500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:1	Aggregate_Molecular_Subtype_Clusters_2014071500	LUSC-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_LUSC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2014071500.0.0	yes
miRseqhc	LUSC-TP.bestclus.txt	gdac.broadinstitute.org_LUSC-TP.miRseq_Clustering_Consensus_Plus.Level_4.2014071500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:1	Aggregate_Molecular_Subtype_Clusters_2014071500	LUSC-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_LUSC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2014071500.0.0	yes
PredictionU133aTCGA	LUSC-TP.bestclus.txt	gdac.broadinstitute.org_LUSC-TP.RPPA_Clustering_CNMF.Level_4.2014071500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10572:1	Aggregate_Molecular_Subtype_Clusters_2014071500	LUSC-TP.mergedcluster.txt	Merged_clusteing	Level_4	txt	gdac.broadinstitute.org_LUSC-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2014071500.0.0	yes
