LinkedOmics
    Analyzing multi-omics data within and across 32 cancer types

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Datasets for Breast invasive carcinoma (TCGA-BRCA)

OMICS Dataset Link Description Level Unit Samples Atrributes File type
Clinical Download Clinical annotation Clinical Phenotype 1097 19 tsi
Phosphoproteome (Site level) Download Phosphoproteome at Site level, data given in log-ratio (normalized) phosphosite Expression (CDAP, Log2ratio) 105 18806 cct
Phosphoproteome (Gene level) Download Phosphoproteome at Gene level, data given in log-ratio (normalized) phosphogene Expression (CDAP, Log2ratio) 105 4765 cct
Proteome (Gene Level) Download Proteome data for tumor samples log-ratio normalized gene Expression (CDAP, Log2ratio) 105 9733 cct
Methylation (CpG-site level, HM27) Download Methylation data at site level for tumor samples (beta values) CpG Beta Values (Val-0.5) 314 25816 cct
Methylation (Gene level, HM27) Download Methylation data of tumor samples at Gene level (Beta values, Illumina HM27 platform) gene Beta Values (Val-0.5) 314 13807 cct
Methylation (CpG-site level, HM450K) Download Methylation data of tumor samples at CpG-site level (Beta values, Illumina HM450K platform) CpG Beta Values (Val-0.5) 783 335854 cct
Methylation (Gene level, HM450K) Download Methylation data of tumor samples at Gene level (Beta values, Illumina HM450K platform) gene Beta Values (Val-0.5) 783 20106 cct
miRNA (GA, Gene level) Download miRNA expression for tumor samples (Illumina GenomeAnalyzer platform, Normalized, miRgene-level, RPM) miRgene Expression (RPM, Log2(Val+1)) 324 754 cct
miRNA (GA, Isoform level) Download miRNA isoform expression for tumor samples (Illumina GenomeAnalyzer platform, Normalized, miRisoform-Level, RPM) miRisoform Expression (RPM, Log2(Val+1)) 324 17365 cct
miRNA (HiSeq, Gene level) Download miRNA expression for tumor samples (Illumina HiSeq platform, Normalized, miRgene-level, RPM) miRgene Expression (RPM, Log2(Val+1)) 755 823 cct
Mutation (Gene level) Download Somatic mutations at gene level SNVs gene Mutation Status (MutSig2CV) 975 7966 cbt
Mutation (Site level) Download Somatic mutations at site level SNVs mutationsite Mutation Status (MutSig2CV) 974 101 cbt
RPPA (Analyte level) Download Reverse phase protein array (RPPA) expression normalized (Analyte-level) analyte Expression (Signal) 887 212 cct
RPPA (Gene level) Download Reverse phase protein array (RPPA) expression normalized (Gene-level) gene Expression (Signal) 887 175 cct
RNAseq (GA, Gene level) Download RNAseq data normalized counts (Illumina GenomeAnalyzer platform, Gene-level, RPKM) gene Expression (RSEM, Log2(Val+1)) 526 6149 cct
RNAseq (HiSeq, Gene level) Download RNAseq data normalized counts (Illumina HiSeq platform, Gene-level, RPKM) gene Expression (RSEM, Log2(Val+1)) 1093 20155 cct
SCNV (Focal level, log-ratio) Download Copy number change at the focal level, GISTIC2 log ratio focal Copy Number Change (GISTIC2, Log2ratio) 1080 69 cct
SCNV (Focal level, Thresholded) Download Copy number change at the focal level, GISTIC2 thresholded focal Copy Number Change (GISTIC2, Log2ratio) 1080 28 cgt
SCNV (Gene level, log-ratio) Download Copy number change at the gene level, GISTIC2 log ratio format gene Copy Number Change (GISTIC2, Log2ratio) 1080 24776 cct
SCNV (Gene level, Thresholded) Download Copy number change at the gene level, GISTIC2 thresholded gene Copy Number Change (GISTIC2, Log2ratio) 1080 24776 cgt

  • *tsi - Mixed data matrix file
  • *cct - continuous data matrix file
  • *cbt - binary data matrix file
  • *cgt - categorical data matrix file