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_selectBestcluster:inputallexp	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.cormatrix.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_selectBestcluster:inputallexp	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.geneheatmap.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_selectBestcluster:inputallexp	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.geneheatmaptopgenes.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_selectBestcluster:inputallexp	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.silfig.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_selectBestcluster:inputallexp	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.consensus.plot.k5.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_selectBestcluster:inputallexp	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.consensus.all.k.plot.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_selectBestcluster:inputallexp	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.consensus.plot.k6.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_selectBestcluster:inputallexp	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.consensus.plot.k8.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_selectBestcluster:inputallexp	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.consensus.plot.k2.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_selectBestcluster:inputallexp	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.cophenetic.coefficient.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_selectBestcluster:inputallexp	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.consensus.plot.k3.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_selectBestcluster:inputallexp	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.consensus.plot.k4.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_selectBestcluster:inputallexp	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.consensus.plot.k7.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_selectBestcluster:inputallexp	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.membership.txt	MolecularSubtypes-Expression_mRNA	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_selectBestcluster:inputallexp	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.bestclus.txt	MolecularSubtypes-Expression_mRNA	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_selectBestcluster:inputallexp	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.subclassmarkers.txt	MolecularSubtypes-Expression_mRNA	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_selectBestcluster:inputallexp	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.normalized.gct	ClusteringInput-Expression_mRNA	Level_4	gct	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_selectBestcluster:inputallexp	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.expclu.gct	ClusteringInput-Expression_mRNA	Level_4	gct	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_selectBestcluster:inputallexp	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_selectBestcluster:inputallexp	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_TopgenesforCluster:expfile	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.cormatrix.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_TopgenesforCluster:expfile	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.geneheatmap.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_TopgenesforCluster:expfile	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.geneheatmaptopgenes.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_TopgenesforCluster:expfile	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.silfig.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_TopgenesforCluster:expfile	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.consensus.plot.k5.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_TopgenesforCluster:expfile	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.consensus.all.k.plot.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_TopgenesforCluster:expfile	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.consensus.plot.k6.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_TopgenesforCluster:expfile	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.consensus.plot.k8.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_TopgenesforCluster:expfile	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.consensus.plot.k2.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_TopgenesforCluster:expfile	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.cophenetic.coefficient.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_TopgenesforCluster:expfile	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.consensus.plot.k3.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_TopgenesforCluster:expfile	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.consensus.plot.k4.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_TopgenesforCluster:expfile	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.consensus.plot.k7.png	MolecularSubtypes-Expression_mRNA	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_TopgenesforCluster:expfile	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.membership.txt	MolecularSubtypes-Expression_mRNA	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_TopgenesforCluster:expfile	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.bestclus.txt	MolecularSubtypes-Expression_mRNA	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_TopgenesforCluster:expfile	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.subclassmarkers.txt	MolecularSubtypes-Expression_mRNA	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_TopgenesforCluster:expfile	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.normalized.gct	ClusteringInput-Expression_mRNA	Level_4	gct	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_TopgenesforCluster:expfile	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	BRCA-TP.expclu.gct	ClusteringInput-Expression_mRNA	Level_4	gct	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_TopgenesforCluster:expfile	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
GDAC_TopgenesforCluster:expfile	BRCA-TP.cn_focal_gistic.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10625:42	CopyNumber_Clustering_CNMF_2016012800	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Clustering_CNMF.Level_4.2016012800.0.0	yes
