TCGA - Prostate adenocarcinoma RNA-Seq
TCGA Prostate adenocarcinoma RNA-Seq data from the Genomic Data Commons (GDC) was generated first by aligning reads to the GRCh38 reference genome. Next, the reads were mapped to each gene with HTSeq count. RNA-Seq expression level read counts were then normalized using the Upper Quartile Fragments Per Kilobase to transcript per Million mapped reads (FPKM-UQ) calculation.
Here are presented the FPKM-UQ expression values for RNA-Seq cases which can be divided to molecular subtypes identified by TCGA Research Network. Four of these seven subtypes are characterized by gene fusions concerning transcription factors ERG, ETV1, ETV4 and FLI1, and the other three are defined by mutations of the SPOP, FOXA1, and IDH1 genes. Some prostate tumors of this analysis could not be categorized into any of the seven molecular subtypes because molecular alterations driving their growth were not identified.