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]
Hotnet_preprocess:lesion	all_lesions.conf_99.txt	gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10468:7	Pathway_Hotnet_2013092300	UCEC-TP.subnetwork_sig_all.txt	significant subnetwork	Level_4	txt	gdac.broadinstitute.org_UCEC-TP.Pathway_Hotnet.Level_4.2013092300.0.0	yes
Hotnet_preprocess:lesion	all_lesions.conf_99.txt	gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10468:7	Pathway_Hotnet_2013092300	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_UCEC-TP.Pathway_Hotnet.Level_4.2013092300.0.0	yes
Hotnet_preprocess:lesion	all_lesions.conf_99.txt	gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10468:7	Pathway_Hotnet_2013092300	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_UCEC-TP.Pathway_Hotnet.Level_4.2013092300.0.0	yes
Hotnet_preprocess:ampfile	amp_genes.conf_99.txt	gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10468:7	Pathway_Hotnet_2013092300	UCEC-TP.subnetwork_sig_all.txt	significant subnetwork	Level_4	txt	gdac.broadinstitute.org_UCEC-TP.Pathway_Hotnet.Level_4.2013092300.0.0	yes
Hotnet_preprocess:ampfile	amp_genes.conf_99.txt	gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10468:7	Pathway_Hotnet_2013092300	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_UCEC-TP.Pathway_Hotnet.Level_4.2013092300.0.0	yes
Hotnet_preprocess:ampfile	amp_genes.conf_99.txt	gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10468:7	Pathway_Hotnet_2013092300	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_UCEC-TP.Pathway_Hotnet.Level_4.2013092300.0.0	yes
Hotnet_preprocess:delfile	del_genes.conf_99.txt	gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10468:7	Pathway_Hotnet_2013092300	UCEC-TP.subnetwork_sig_all.txt	significant subnetwork	Level_4	txt	gdac.broadinstitute.org_UCEC-TP.Pathway_Hotnet.Level_4.2013092300.0.0	yes
Hotnet_preprocess:delfile	del_genes.conf_99.txt	gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10468:7	Pathway_Hotnet_2013092300	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_UCEC-TP.Pathway_Hotnet.Level_4.2013092300.0.0	yes
Hotnet_preprocess:delfile	del_genes.conf_99.txt	gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10468:7	Pathway_Hotnet_2013092300	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_UCEC-TP.Pathway_Hotnet.Level_4.2013092300.0.0	yes
Hotnet_preprocess:mutfile	UCEC-TP.per_gene.mutation_counts.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10468:7	Pathway_Hotnet_2013092300	UCEC-TP.subnetwork_sig_all.txt	significant subnetwork	Level_4	txt	gdac.broadinstitute.org_UCEC-TP.Pathway_Hotnet.Level_4.2013092300.0.0	yes
Hotnet_preprocess:mutfile	UCEC-TP.per_gene.mutation_counts.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10468:7	Pathway_Hotnet_2013092300	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_UCEC-TP.Pathway_Hotnet.Level_4.2013092300.0.0	yes
Hotnet_preprocess:mutfile	UCEC-TP.per_gene.mutation_counts.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10468:7	Pathway_Hotnet_2013092300	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_UCEC-TP.Pathway_Hotnet.Level_4.2013092300.0.0	yes
