| DGE |
1 + 2 |
Differential gene expression data. This is expression data that was generated using DMAGE (Deep Multiplex Analysis of Gene Expression). Available for TCGA-OV project. |
| exon |
3 |
Exon-level expression data. Includes exon quantification (raw counts and RPKM) and junction quantification (raw counts). |
| FIRMA |
3 |
Subset of gene expression: finding isoforms using robust multichip analysis. Available for TCGA-OV, GBM, LUSC projects. |
| gene |
3 |
Gene-level expression data. This includes data from both mRNA (raw count and RSEM) and miRNA (raw count and RPKM). Total RNA-Seq data is also included (raw count and RSEM) in which all types of RNA were quantified. All expression data is available as normalized or unnormalized. Some exon array data files are also included in this tag. |
| indel |
2 |
VCF files that only include insertion-deletion mutations. |
| isoform |
3 |
Gene expression isoform data. This includes data from both mRNA (raw count and RSEM) and miRNA (raw count and RPKM) expression. Total RNA-Seq data is also included (raw count and RSEM) in which all types of RNA were quantified. All expression data is available as normalized or unnormalized. |
| junction |
3 |
Exon junction quantification data. This includes only data from RNA-Seq or total RNA-Seq. Expression levels are measured in raw counts. |
| normalized |
3 |
Normalized expression levels measured in RSEM. Includes gene and isoform level data. |
| snv |
2 |
Simple nucleotide variation files measured with DNA or RNA-Seq. These are available as VCFs or MAFs. This tag does not include VCF and MAF files from copy number variation or bisulfite-seq studies. |
| sv |
2 |
Structural rearrangement files. Available in FASTA and VCF format. The VCF files contain structural variants identified from RNA-Seq data. FASTA files contain contig sequences that are referenced by the VCF file. Available for TCGA – OV, STAD, ESCA, LAML. |
| unnormalized |
3 |
Raw expression levels measured in RSEM. Includes gene and isoform level data. |
| v1 |
3 |
RNA-SeqV1 expression data. Includes gene, exon and junction expression data. No miRNA-Seq data is included. |
| v2 |
3 |
RNA-SeqV2 expression data. Includes gene, exon, isoform, and junction expression data. No miRNA-Seq data is included. |