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]
getCNExpCorrelation:reducedseg	all_data_by_genes.txt	gdac.broadinstitute.org_READ-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00289:57	Correlate_CopyNumber_vs_mRNA_2014071500	READ-TP.CORS.tsv	Correlation_result	Level_4	tsv	gdac.broadinstitute.org_READ-TP.Correlate_CopyNumber_vs_mRNA.Level_4.2014071500.0.0	yes
getCNExpCorrelation:reducedseg	all_data_by_genes.txt	gdac.broadinstitute.org_READ-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00289:57	Correlate_CopyNumber_vs_mRNA_2014071500	STATS.QA.tsv	Correlation_result	Level_4	tsv	gdac.broadinstitute.org_READ-TP.Correlate_CopyNumber_vs_mRNA.Level_4.2014071500.0.0	yes
getCNExpCorrelation:reducedseg	all_data_by_genes.txt	gdac.broadinstitute.org_READ-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00289:57	Correlate_CopyNumber_vs_mRNA_2014071500	OUTPUT.CORS.png	Correlation-CopyNumber_Expression_miRNA	Level_4	png	gdac.broadinstitute.org_READ-TP.Correlate_CopyNumber_vs_mRNA.Level_4.2014071500.0.0	yes
getCNExpCorrelation:reducedseg	all_data_by_genes.txt	gdac.broadinstitute.org_READ-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00289:57	Correlate_CopyNumber_vs_mRNA_2014071500	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_READ-TP.Correlate_CopyNumber_vs_mRNA.Level_4.2014071500.0.0	yes
getCNExpCorrelation:reducedseg	all_data_by_genes.txt	gdac.broadinstitute.org_READ-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00289:57	Correlate_CopyNumber_vs_mRNA_2014071500	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_READ-TP.Correlate_CopyNumber_vs_mRNA.Level_4.2014071500.0.0	yes
getCNExpCorrelation:mrnaexp	READ-TP.medianexp.txt	gdac.broadinstitute.org_READ-TP.mRNA_Preprocess_Median.Level_3.0.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00289:57	Correlate_CopyNumber_vs_mRNA_2014071500	READ-TP.CORS.tsv	Correlation_result	Level_4	tsv	gdac.broadinstitute.org_READ-TP.Correlate_CopyNumber_vs_mRNA.Level_4.2014071500.0.0	yes
getCNExpCorrelation:mrnaexp	READ-TP.medianexp.txt	gdac.broadinstitute.org_READ-TP.mRNA_Preprocess_Median.Level_3.0.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00289:57	Correlate_CopyNumber_vs_mRNA_2014071500	STATS.QA.tsv	Correlation_result	Level_4	tsv	gdac.broadinstitute.org_READ-TP.Correlate_CopyNumber_vs_mRNA.Level_4.2014071500.0.0	yes
getCNExpCorrelation:mrnaexp	READ-TP.medianexp.txt	gdac.broadinstitute.org_READ-TP.mRNA_Preprocess_Median.Level_3.0.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00289:57	Correlate_CopyNumber_vs_mRNA_2014071500	OUTPUT.CORS.png	Correlation-CopyNumber_Expression_miRNA	Level_4	png	gdac.broadinstitute.org_READ-TP.Correlate_CopyNumber_vs_mRNA.Level_4.2014071500.0.0	yes
getCNExpCorrelation:mrnaexp	READ-TP.medianexp.txt	gdac.broadinstitute.org_READ-TP.mRNA_Preprocess_Median.Level_3.0.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00289:57	Correlate_CopyNumber_vs_mRNA_2014071500	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_READ-TP.Correlate_CopyNumber_vs_mRNA.Level_4.2014071500.0.0	yes
getCNExpCorrelation:mrnaexp	READ-TP.medianexp.txt	gdac.broadinstitute.org_READ-TP.mRNA_Preprocess_Median.Level_3.0.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00289:57	Correlate_CopyNumber_vs_mRNA_2014071500	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_READ-TP.Correlate_CopyNumber_vs_mRNA.Level_4.2014071500.0.0	yes
