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_TopgenesforCluster1.expfile	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	BRCA.cormatrix.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_TopgenesforCluster1.expfile	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	BRCA.geneheatmap.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_TopgenesforCluster1.expfile	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	cnmf.consensus.plot.k4.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_TopgenesforCluster1.expfile	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	cnmf.consensus.plot.k2.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_TopgenesforCluster1.expfile	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	cnmf.consensus.plot.k8.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_TopgenesforCluster1.expfile	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	cnmf.consensus.plot.k5.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_TopgenesforCluster1.expfile	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	cnmf.consensus.plot.k6.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_TopgenesforCluster1.expfile	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	BRCA.silfig.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_TopgenesforCluster1.expfile	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	BRCA.geneheatmaptopgenes.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_TopgenesforCluster1.expfile	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	cnmf.consensus.plot.k3.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_TopgenesforCluster1.expfile	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	cnmf.consensus.all.k.plot.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_TopgenesforCluster1.expfile	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	cnmf.consensus.plot.k7.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_TopgenesforCluster1.expfile	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	cnmf.cophenetic.coefficient.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_TopgenesforCluster1.expfile	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	cnmf.membership.txt	MolecularSubtypes-Expression_mRNA	Level_4	text	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_TopgenesforCluster1.expfile	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	BRCA.bestclus.txt	MolecularSubtypes-Expression_mRNA	Level_4	text	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_TopgenesforCluster1.expfile	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	BRCA.subclassmarkers.txt	MolecularSubtypes-Expression_mRNA	Level_4	text	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_TopgenesforCluster1.expfile	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	outputprefix.expclu.gct	ClusteringInput-Expression_mRNA	Level_4	gct	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_TopgenesforCluster1.expfile	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	cnmf.normalized.gct	ClusteringInput-Expression_mRNA	Level_4	gct	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_TopgenesforCluster1.expfile	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_TopgenesforCluster1.expfile	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	BRCA.cormatrix.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	BRCA.geneheatmap.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	cnmf.consensus.plot.k4.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	cnmf.consensus.plot.k2.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	cnmf.consensus.plot.k8.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	cnmf.consensus.plot.k5.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	cnmf.consensus.plot.k6.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	BRCA.silfig.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	BRCA.geneheatmaptopgenes.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	cnmf.consensus.plot.k3.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	cnmf.consensus.all.k.plot.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	cnmf.consensus.plot.k7.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	cnmf.cophenetic.coefficient.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	cnmf.membership.txt	MolecularSubtypes-Expression_mRNA	Level_4	text	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	BRCA.bestclus.txt	MolecularSubtypes-Expression_mRNA	Level_4	text	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	BRCA.subclassmarkers.txt	MolecularSubtypes-Expression_mRNA	Level_4	text	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	outputprefix.expclu.gct	ClusteringInput-Expression_mRNA	Level_4	gct	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	cnmf.normalized.gct	ClusteringInput-Expression_mRNA	Level_4	gct	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	BRCA.miRseq_RPKM_tmm_log2.txt	gdac.broadinstitute.org_BRCA.miRseq_Preprocess.Level_4.2012052500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:33	miRseq_Clustering_CNMF_2012052500	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_BRCA.miRseq_Clustering_CNMF.Level_4.2012052500.0.0	yes
