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	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	outputprefix.expclu.gct	ClusteringInput-Expression_mRNA	Level_4	gct	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_TopgenesforCluster1.expfile	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	cnmf.normalized.gct	ClusteringInput-Expression_mRNA	Level_4	gct	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_TopgenesforCluster1.expfile	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	cnmf.consensus.plot.k7.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_TopgenesforCluster1.expfile	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	cnmf.consensus.plot.k8.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_TopgenesforCluster1.expfile	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	cnmf.consensus.plot.k2.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_TopgenesforCluster1.expfile	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	cnmf.consensus.plot.k3.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_TopgenesforCluster1.expfile	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	OV.geneheatmap.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_TopgenesforCluster1.expfile	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	cnmf.consensus.plot.k4.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_TopgenesforCluster1.expfile	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	cnmf.cophenetic.coefficient.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_TopgenesforCluster1.expfile	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	cnmf.consensus.plot.k5.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_TopgenesforCluster1.expfile	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	OV.cormatrix.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_TopgenesforCluster1.expfile	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	cnmf.consensus.all.k.plot.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_TopgenesforCluster1.expfile	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	cnmf.consensus.plot.k6.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_TopgenesforCluster1.expfile	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	OV.silfig.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_TopgenesforCluster1.expfile	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	OV.geneheatmaptopgenes.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_TopgenesforCluster1.expfile	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	cnmf.membership.txt	MolecularSubtypes-Expression_mRNA	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_TopgenesforCluster1.expfile	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	OV.bestclus.txt	MolecularSubtypes-Expression_mRNA	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_TopgenesforCluster1.expfile	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	OV.subclassmarkers.txt	MolecularSubtypes-Expression_mRNA	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_TopgenesforCluster1.expfile	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_TopgenesforCluster1.expfile	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	outputprefix.expclu.gct	ClusteringInput-Expression_mRNA	Level_4	gct	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	cnmf.normalized.gct	ClusteringInput-Expression_mRNA	Level_4	gct	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	cnmf.consensus.plot.k7.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	cnmf.consensus.plot.k8.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	cnmf.consensus.plot.k2.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	cnmf.consensus.plot.k3.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	OV.geneheatmap.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	cnmf.consensus.plot.k4.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	cnmf.cophenetic.coefficient.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	cnmf.consensus.plot.k5.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	OV.cormatrix.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	cnmf.consensus.all.k.plot.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	cnmf.consensus.plot.k6.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	OV.silfig.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	OV.geneheatmaptopgenes.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	cnmf.membership.txt	MolecularSubtypes-Expression_mRNA	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	OV.bestclus.txt	MolecularSubtypes-Expression_mRNA	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	OV.subclassmarkers.txt	MolecularSubtypes-Expression_mRNA	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
GDAC_CNMFselectcluster3.inputallexp	OV.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00415:72	CopyNumber_Clustering_CNMF_2012102400	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_OV.CopyNumber_Clustering_CNMF.Level_4.2012102400.0.0	yes
