4.7 Article

Recounting the FANTOM CAGE-Associated Transcriptome

期刊

GENOME RESEARCH
卷 30, 期 7, 页码 1073-1081

出版社

COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1101/gr.254656.119

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资金

  1. National Institutes of Health-National Cancer Institute (NIH-NCI) [P30CA006973, 1U01CA231776, U01CA196390, R01CA200859]
  2. National Institutes of Health-National Institute of General Medical Sciences (NIH-NIGMS) [R01GM118568, R21MH109956-01]
  3. U.S. Department of Defense (DoD) office of the Congressionally Directed Medical Research Programs (CDMRP) [W81XWH-16-1-0739]
  4. Russian Academic project [0112-2019-0001]
  5. Russian Foundation for Basic Research project [17-00-00208]
  6. Fundacao de Amparo a Pesquisa do Estado de Minas Gerais [BDS-00493-16]
  7. National Science Foundation [ACI-1261715]

向作者/读者索取更多资源

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.

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