Title | Recounting the FANTOM CAGE-Associated Transcriptome. |
Publication Type | Journal Article |
Year of Publication | 2020 |
Authors | Imada 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 |
Journal | Genome Res |
Volume | 30 |
Issue | 7 |
Pagination | 1073-1081 |
Date Published | 2020 07 |
ISSN | 1549-5469 |
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. |
DOI | 10.1101/gr.254656.119 |
Alternate Journal | Genome Res |
PubMed ID | 32079618 |
PubMed Central ID | PMC7397872 |
Grant List | P30 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 Lab:
Related Faculty:
Luigi Marchionni, M.D., Ph.D.