microRNA ExpressionΒΆ
The current ISB TCGA data pipeline uses a Perl script
expression\_matrix\_mimat.pl provided by BCGSC which reads the
isoform data files and outputs expression values for “mature microRNAs”.
This output matrix contains a consistent number of mature microRNAs,
referred to using a combination of the microRNA
gene name and the unique accession number, eg:
“hsa-mir-21.MIMAT0000076”. During ETL, this string is split into two
parts and stored as separate columns in the BigQuery
table.
The entire matrix is then melted into a flat structure (known as the tidy data format) and loaded
into the table.
Only the isoform files matching the pattern
%.isoform.quantification.txt and containing hg19 data were used. The aliquot barcode
information was obtained from the SDRF file associated with the Level-3
isoform data file.