A new study describing our FC-R2 (for: “FANTOM-CAT recount2”) resource is out in Genome Research. FC-R2 is a new quantification of the recount2 summaries using the more inclusive annotation produced by the FANTOM CAGE-Associated Transcriptome (FANTOM-CAT) project. This annotation consists of over 109,000 coding and noncoding genes. By combining this annotation with the recount2 resource, we now provide quantifications for that wide array of genes for over 70,000 human RNA-seq samples. The summaries that comprise the FC-R2 resource are available through the recount2 interface.
To show the utility of the new resource, we use it to (a) identify tissue-specific transcription profiles for distinct classes of coding and noncoding genes, (b) perform differential expression analysis across thirteen cancer types, identifying novel noncoding genes potentially involved in tumor pathogenesis and progression, and (c) confirm the prognostic value for several enhancers lncRNAs expression in cancer.
This study was a collaboration with Dr. Luigi Marchionni and his excellent group. Congratulations especially to Eddie Imada and Dr. Diego Sanchez, as well as to Leo Collado Torres and Chris Wilks.