RT Journal
A1 Imada, Eddie Luidy
A1 Sanchez, Diego Fernando
A1 Collado-Torres, Leonardo
A1 Wilks, Christopher
A1 Matam, Tejasvi
A1 Dinalankara, Wikum
A1 Stupnikov, Aleksey
A1 Lobo-Pereira, Francisco
A1 Yip, Chi-Wai
A1 Yasuzawa, Kayoko
A1 Kondo, Naoto
A1 Itoh, Masayoshi
A1 Suzuki, Harukazu
A1 Kasukawa, Takeya
A1 Hon, Chung-Chau
A1 de Hoon, Michiel J.L.
A1 Shin, Jay W.
A1 Carninci, Piero
A1 Jaffe, Andrew E.
A1 Leek, Jeffrey T.
A1 Favorov, Alexander
A1 Franco, Gloria R.
A1 Langmead, Ben
A1 Marchionni, Luigi
T1 Recounting the FANTOM CAGE-Associated Transcriptome
JF Genome Research 
JO Genome Research 
YR 2020 
FD July 01 
VO 30 
IS 7 
SP 1073 
OP 1081 
DO 10.1101/gr.254656.119 
UL http://genome.cshlp.org/content/30/7/1073.abstract 
AB Long noncoding RNAs (lncRNAs) have emerged as key coordinators of biological and cellular processes. Characterizing lncRNA expression across cells and tissues is key to understanding their role in determining phenotypes, including human diseases. We present here FC-R2, a comprehensive expression atlas across a broadly defined human transcriptome, inclusive of over 109,000 coding and noncoding genes, as described in the FANTOM CAGE-Associated Transcriptome (FANTOM-CAT) study. This atlas greatly extends the gene annotation used in the original recount2 resource. We demonstrate the utility of the FC-R2 atlas by reproducing key findings from published large studies and by generating new results across normal and diseased human samples. In particular, we (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 enhancer lncRNAs expression in cancer. Our resource is instrumental for the systematic molecular characterization of lncRNA by the FANTOM6 Consortium. In conclusion, comprised of over 70,000 samples, the FC-R2 atlas will empower other researchers to investigate functions and biological roles of both known coding genes and novel lncRNAs.