TY  - JOUR
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
Y1  - 2020/07/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1073 
EP  - 1081 
DO  - 10.1101/gr.254656.119 
VL  - 30 
IS  - 7 
UR  - http://genome.cshlp.org/content/30/7/1073.abstract 
N2  - 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. 
ER  -