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

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Datasets for Head and Neck squamous cell carcinoma (TCGA-HNSC)

OMICS Dataset Link Description Level Unit Samples Atrributes File type
Clinical Download Clinical annotation Clinical Phenotype 528 14 tsi
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) 528 336523 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) 528 20114 cct
miRNA (GA, miRgene level) Download miRNA expression for tumor samples (Illumina GenomeAnalyzer platform, miRgene-level, Normalized, RPM) miRgene Expression (RPM, Log2(Val+1)) 37 633 cct
miRNA (isoform level) Download miRNA isoform expression for tumor samples (Normalized, RPM) miRisoform Expression (RPM, Log2(Val+1)) 37 9376 cct
miRNA (HiSeq, miRgene level) Download miRNA expression for tumor samples (Illumina HiSeq platform, miRgene-level, Normalized, RPM) miRgene Expression (RPM, Log2(Val+1)) 486 842 cct
Mutation (Gene level) Download Somatic mutations at gene level SNVs gene Mutation Status (MutSig2CV) 511 9434 cbt
Mutation (Site level) Download Somatic mutations at site level SNVs mutationsite Mutation Status (MutSig2CV) 511 18 cbt
RPPA (Analyte Level) Download Reverse phase protein array (RPPA) expression normalized (Analyte-level) analyte Expression (Signal) 212 149 cct
RPPA (Gene Level) Download Reverse phase protein array (RPPA) expression normalized (Gene-level) gene Expression (Signal) 212 125 cct
RNAseq (HiSeq, Gene level) Download RNAseq data normalized counts (Illumina HiSeq platform, Gene-level, Normalized log2 RPKM) gene Expression (RSEM, Log2(Val+1)) 520 20164 cct
SCNV (Focal level, log-ratio) Download Copy number change at the focal level, GISTIC2 log ratio focal Copy Number Change (GISTIC2, Log2ratio) 522 74 cct
SCNV (Focal level, Thresholded) Download Copy number change at the focal level, GISTIC2 thresholded focal Copy Number Change (GISTIC2, Log2ratio) 522 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) 522 24776 cct
SCNV (Gene level, Thresholded) Download Copy number change at the gene level, GISTIC2 thresholded gene Copy Number Change (GISTIC2, Log2ratio) 522 24776 cgt

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