TY - JOUR
T1 - Recounting the FANTOM CAGE-Associated Transcriptome
AU - Imada, Eddie Luidy
AU - Sanchez, Diego Fernando
AU - Collado-Torres, Leonardo
AU - Wilks, Christopher
AU - Matam, Tejasvi
AU - Dinalankara, Wikum
AU - Stupnikov, Aleksey
AU - Lobo-Pereira, Francisco
AU - Yip, Chi Wai
AU - Yasuzawa, Kayoko
AU - Kondo, Naoto
AU - Itoh, Masayoshi
AU - Suzuki, Harukazu
AU - Kasukawa, Takeya
AU - Hon, Chung Chau
AU - De Hoon, Michiel J.L.
AU - Shin, Jay W.
AU - Carninci, Piero
AU - Jaffe, Andrew E.
AU - Leek, Jeffrey T.
AU - Favorov, Alexander
AU - Franco, Gloria R.
AU - Langmead, Ben
AU - Marchionni, Luigi
N1 - Publisher Copyright:
© 2020 Imada et al.
PY - 2020/7
Y1 - 2020/7
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 (FANTOMCAT) 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.
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 (FANTOMCAT) 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.
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U2 - 10.1101/gr.254656.119
DO - 10.1101/gr.254656.119
M3 - Article
C2 - 32079618
AN - SCOPUS:85089202510
SN - 1088-9051
VL - 30
SP - 1073
EP - 1081
JO - Genome research
JF - Genome research
IS - 7
ER -