mRNA Expression¶
Gene expression data for the TCGA project has been produced by two different centers, using several different platforms and fundamentally different pipelines. Most of the data, from each center, was produced using the Illumina HiSeq platform and for that reason the first two BigQuery tables containing gene expression data are based on those specific subsets of the TCGA mRNA expression data:
- the majority of the data was produced by the UNC LCCC and the resulting normalized RSEM values are stored in one table
- and a subset of the data was produced by the BC GSC and the resulting normalized RPKM values are stored in another table
UNC RNAseqV2 Pipeline¶
A DESCRIPTION.txt file describing the algorithms,
methods, and protocols used to produce the Level-1, Level-2, and Level-3 data
can be obtained from the TCGA DCC.
The BigQuery table was populated using the values in files matching the pattern
%.rsem.genes.normalized\_results. These raw “RSEM genes normalized results”
files have two columns, both of which are stored in the BigQuery table. The first
column contains the gene_id which contains two parts separated by a |, eg: TP53|7157.
The second column contains the normalized_count representing the expression value for that gene.
The gene\_id column is split into two components and stored as separate columns:
original\_gene\_symbol and gene\_id. Based on the gene_id, the current HGNC approved
gene symbol is
looked up
and added as a third column: HGNC_gene_symbol.
BCGSC RNAseq Pipeline¶
A DESCRIPTION.txt file describing the algorithms,
methods, and protocols used to produce the Level-1, Level-2, and Level-3 data
can be obtained from the TCGA DCC.
The BigQuery table was populated using the values in files matching the pattern
%.gene.quantification.txt. These raw “gene quantification” files have
four columns: gene, raw\_counts, median\_length\_normalized, and RPKM.
From these the gene and the RPKM values are stored in the BigQuery table.
The gene string contains either two or three parts, similarly
separated by a \|, eg TP53\|7157\_calculated or Mir\_1302\|?\|3of7\_calculated.
The gene string is split into two or three components and stored as separate columns:
original_gene_symbol and gene_id and, if there is a third component, a gene_addenda column.
If one component is simply ?, that character string is replaced by a NULL value.
Finally, the current HGNC approved gene symbol is
looked up
and added as an additonal column: HGNC_gene_symbol.