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]
GDAC_TopgenesforCluster1.expfile	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	cnmf.consensus.plot.k5.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_TopgenesforCluster1.expfile	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	cnmf.consensus.all.k.plot.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_TopgenesforCluster1.expfile	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	cnmf.consensus.plot.k7.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_TopgenesforCluster1.expfile	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	cnmf.consensus.plot.k8.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_TopgenesforCluster1.expfile	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	COADREAD.cormatrix.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_TopgenesforCluster1.expfile	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	cnmf.consensus.plot.k6.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_TopgenesforCluster1.expfile	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	cnmf.cophenetic.coefficient.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_TopgenesforCluster1.expfile	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	cnmf.consensus.plot.k2.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_TopgenesforCluster1.expfile	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	COADREAD.geneheatmaptopgenes.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_TopgenesforCluster1.expfile	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	cnmf.consensus.plot.k4.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_TopgenesforCluster1.expfile	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	COADREAD.silfig.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_TopgenesforCluster1.expfile	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	cnmf.consensus.plot.k3.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_TopgenesforCluster1.expfile	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	COADREAD.geneheatmap.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_TopgenesforCluster1.expfile	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	COADREAD.bestclus.txt	MolecularSubtypes-Expression_mRNA	Level_4	text	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_TopgenesforCluster1.expfile	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	COADREAD.subclassmarkers.txt	MolecularSubtypes-Expression_mRNA	Level_4	text	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_TopgenesforCluster1.expfile	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_TopgenesforCluster1.expfile	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_CNMFselectcluster3.inputallexp	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	cnmf.consensus.plot.k5.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_CNMFselectcluster3.inputallexp	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	cnmf.consensus.all.k.plot.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_CNMFselectcluster3.inputallexp	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	cnmf.consensus.plot.k7.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_CNMFselectcluster3.inputallexp	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	cnmf.consensus.plot.k8.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_CNMFselectcluster3.inputallexp	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	COADREAD.cormatrix.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_CNMFselectcluster3.inputallexp	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	cnmf.consensus.plot.k6.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_CNMFselectcluster3.inputallexp	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	cnmf.cophenetic.coefficient.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_CNMFselectcluster3.inputallexp	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	cnmf.consensus.plot.k2.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_CNMFselectcluster3.inputallexp	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	COADREAD.geneheatmaptopgenes.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_CNMFselectcluster3.inputallexp	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	cnmf.consensus.plot.k4.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_CNMFselectcluster3.inputallexp	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	COADREAD.silfig.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_CNMFselectcluster3.inputallexp	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	cnmf.consensus.plot.k3.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_CNMFselectcluster3.inputallexp	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	COADREAD.geneheatmap.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_CNMFselectcluster3.inputallexp	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	COADREAD.bestclus.txt	MolecularSubtypes-Expression_mRNA	Level_4	text	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_CNMFselectcluster3.inputallexp	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	COADREAD.subclassmarkers.txt	MolecularSubtypes-Expression_mRNA	Level_4	text	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_CNMFselectcluster3.inputallexp	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
GDAC_CNMFselectcluster3.inputallexp	COADREAD.medianexp.txt	gdac.broadinstitute.org_COADREAD.mRNA_Preprocess_Median.Level_4.2012032100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:32	mRNA_Clustering_CNMF_2012032100	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_COADREAD.mRNA_Clustering_CNMF.Level_4.2012032100.0.0
