Year: 2020
Type: preprint
Abstract: ABSTRACT Long non-coding 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 non-coding 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 non-coding genes, (b) perform differential expression analyses across thirteen cancer types, providing new insights linking promoter and enhancer lncRNAs expression to tumor pathogenesis, and (c) confirm the prognostic value of several enhancers in cancer. 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. Most importantly, access to the FC-R2 atlas is available from https://jhubiostatistics.shinyapps.io/recount/ , the recount Bioconductor package, and http://marchionnilab.org/fcr2.html .
Source: Genome Research
Authors: Eddie-Luidy Imada, Diego Fernando Sanchez, Leonardo Collado-Torres, Christopher Wilks, Tejasvi Matam, Wikum Dinalankara, Aleksey Stupnikov, Francisco Lobo-Pereira, Chi-Wai Yip, Kayoko Yasuzawa, Naoto Kondo, Masayoshi Itoh, Harukazu Suzuki, Takeya Kasukawa, Chung-Chau Hon, Michiel JL de Hoon, Jay W Shin, Piero Carninci, Andrew E Jaffe, Jeffrey T Leek, Alexander Favorov, Gloria R Franco, Ben Langmead, Luigi Marchionni
Language: English
Subfield: Cancer Research
Domain: Life Sciences
Open Access status: hybrid
Funders: National Science Foundation, U.S. Department of Defense, Johns Hopkins University, Russian Foundation for Basic Research, National Institutes of Health, National Institute of Mental Health, National Cancer Institute, National Institute of General Medical Sciences, National Institute of Dental and Craniofacial Research, Congressionally Directed Medical Research Programs
Awards: G1165598027, G1570158730, Regional Oncology Research Center (American Eurasian Cancer Alliance Supplement), DEVELOPING A PTEN-ERG SIGNATURE TO IMPROVE MOLECULAR RISK STRATIFICATION IN PROSTATE CANCER, G2033312956, G21146293, G2580177631, Hardwiring Mechanism into Predicting Cancer Phenotypes by Computational Learning, Developing a PTEN-ERG Signature to Improve Molecular Risk Stratification in Prostate Cancer, G3032705448, G3310038711, CIF21 DIBBs: Long Term Access to Large Scientific Data Sets: The SkyServer and Beyond, G4119534169, G4298445392, G4308351639, G465951118, G4950536974, G5389860395, G5728511275, G5850682332, G6405588829, Bioinformatic-Chemical Approach to Credential Molecular Targets to Combat Rapid Chemo-Radiation Resistance in SCLC, Delineating chromatin-related gene expression signatures as a function of HNSCC progression, G7216376094, G9000041231, G9000130411, G9000133668, G9000260947
OpenAlex ID: W3006757803