Recounting the FANTOM CAGE-Associated Transcriptome.

TitleRecounting the FANTOM CAGE-Associated Transcriptome.
Publication TypeJournal Article
Year of Publication2020
AuthorsImada ELuidy, Sanchez DFernando, Collado-Torres L, Wilks C, Matam T, Dinalankara W, Stupnikov A, Lobo-Pereira F, Yip C-W, Yasuzawa K, Kondo N, Itoh M, Suzuki H, Kasukawa T, Hon C-C, de Hoon MJL, Shin JW, Carninci P, Jaffe AE, Leek JT, Favorov A, Franco GR, Langmead B, Marchionni L
JournalGenome Res
Volume30
Issue7
Pagination1073-1081
Date Published2020 07
ISSN1549-5469
Abstract

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 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.

DOI10.1101/gr.254656.119
Alternate JournalGenome Res
PubMed ID32079618
PubMed Central IDPMC7397872
Grant ListP30 CA006973 / CA / NCI NIH HHS / United States
U01 CA196390 / CA / NCI NIH HHS / United States
R21 MH109956 / MH / NIMH NIH HHS / United States
U01 CA231776 / CA / NCI NIH HHS / United States
R01 CA200859 / CA / NCI NIH HHS / United States
R01 GM118568 / GM / NIGMS NIH HHS / United States
R01 DE027809 / DE / NIDCR NIH HHS / United States
Related Faculty: 
Luigi Marchionni, M.D., Ph.D.

Pathology & Laboratory Medicine 1300 York Avenue New York, NY 10065 Phone: (212) 746-6464
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