mRNA Expression¶
Although gene expression data for the TCGA project was produced by two different centers, only the data produced by the UNC RSEM pipeline was incorporated into the GDC. The GDC has also reprocessed that data against HG38 resulting in a second BigQuery table.:
- the data produced by the UNC LCCC and the resulting normalized RSEM values are stored in one table
- and the data produced by the GDC 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.
GDC RNAseq Pipeline¶
The original DCC genomic data was reprocessed against the HG38 genomic build.
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 additional column: HGNC_gene_symbol.