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]
ClinicalAnalysisAllGenes_new1.data.file	THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_THCA-TP.mRNAseq_Preprocess.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	THCA-TP.clin.merged.picked.clindata.txt	clinical_Correlation-Clinical_Expression	Level_4	text	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.data.file	THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_THCA-TP.mRNAseq_Preprocess.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	table9.txt	clinical_Correlation-Clinical_Expression	Level_4	text	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.data.file	THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_THCA-TP.mRNAseq_Preprocess.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	table3.txt	clinical_Correlation-Clinical_Expression	Level_4	text	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.data.file	THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_THCA-TP.mRNAseq_Preprocess.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	table1.txt	clinical_Correlation-Clinical_Expression	Level_4	text	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.data.file	THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_THCA-TP.mRNAseq_Preprocess.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	table5.txt	clinical_Correlation-Clinical_Expression	Level_4	text	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.data.file	THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_THCA-TP.mRNAseq_Preprocess.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	table7.txt	clinical_Correlation-Clinical_Expression	Level_4	text	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.data.file	THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_THCA-TP.mRNAseq_Preprocess.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	table11.txt	clinical_Correlation-Clinical_Expression	Level_4	text	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.data.file	THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_THCA-TP.mRNAseq_Preprocess.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	supp.table1.txt	clinical_Correlation-Clinical_Expression	Level_4	text	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.data.file	THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_THCA-TP.mRNAseq_Preprocess.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	V5ex.png	clinical_Correlation-Clinical_Expression	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.data.file	THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_THCA-TP.mRNAseq_Preprocess.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	V1ex.png	clinical_Correlation-Clinical_Expression	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.data.file	THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_THCA-TP.mRNAseq_Preprocess.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	V2ex.png	clinical_Correlation-Clinical_Expression	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.data.file	THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_THCA-TP.mRNAseq_Preprocess.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	V3ex.png	clinical_Correlation-Clinical_Expression	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.data.file	THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_THCA-TP.mRNAseq_Preprocess.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	V4ex.png	clinical_Correlation-Clinical_Expression	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.data.file	THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_THCA-TP.mRNAseq_Preprocess.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.data.file	THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_THCA-TP.mRNAseq_Preprocess.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.clinical.file	THCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_THCA-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	THCA-TP.clin.merged.picked.clindata.txt	clinical_Correlation-Clinical_Expression	Level_4	text	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.clinical.file	THCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_THCA-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	table9.txt	clinical_Correlation-Clinical_Expression	Level_4	text	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.clinical.file	THCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_THCA-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	table3.txt	clinical_Correlation-Clinical_Expression	Level_4	text	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.clinical.file	THCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_THCA-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	table1.txt	clinical_Correlation-Clinical_Expression	Level_4	text	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.clinical.file	THCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_THCA-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	table5.txt	clinical_Correlation-Clinical_Expression	Level_4	text	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.clinical.file	THCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_THCA-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	table7.txt	clinical_Correlation-Clinical_Expression	Level_4	text	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.clinical.file	THCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_THCA-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	table11.txt	clinical_Correlation-Clinical_Expression	Level_4	text	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.clinical.file	THCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_THCA-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	supp.table1.txt	clinical_Correlation-Clinical_Expression	Level_4	text	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.clinical.file	THCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_THCA-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	V5ex.png	clinical_Correlation-Clinical_Expression	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.clinical.file	THCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_THCA-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	V1ex.png	clinical_Correlation-Clinical_Expression	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.clinical.file	THCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_THCA-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	V2ex.png	clinical_Correlation-Clinical_Expression	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.clinical.file	THCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_THCA-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	V3ex.png	clinical_Correlation-Clinical_Expression	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.clinical.file	THCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_THCA-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	V4ex.png	clinical_Correlation-Clinical_Expression	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.clinical.file	THCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_THCA-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
ClinicalAnalysisAllGenes_new1.clinical.file	THCA-TP.clin.merged.picked.txt	gdac.broadinstitute.org_THCA-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00337:26	Correlate_Clinical_vs_mRNAseq_2012122100	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_mRNAseq.Level_4.2012122100.0.0	yes
