Recounting the FANTOM CAGE-Associated Transcriptome
- Eddie Luidy Imada1,2,11,
- Diego Fernando Sanchez1,11,
- Leonardo Collado-Torres3,
- Christopher Wilks4,
- Tejasvi Matam1,
- Wikum Dinalankara1,
- Aleksey Stupnikov1,
- Francisco Lobo-Pereira5,
- Chi-Wai Yip6,
- Kayoko Yasuzawa6,
- Naoto Kondo6,
- Masayoshi Itoh7,
- Harukazu Suzuki6,
- Takeya Kasukawa6,
- Chung-Chau Hon6,
- Michiel J.L. de Hoon6,
- Jay W. Shin6,
- Piero Carninci6,
- Andrew E. Jaffe3,8,9,
- Jeffrey T. Leek9,
- Alexander Favorov1,10,
- Gloria R. Franco2,
- Ben Langmead4,9,11 and
- Luigi Marchionni1,11
- 1Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21827, USA;
- 2Departamento de Bioqúımica e Imunologia, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil;
- 3Lieber Institute for Brain Development, Baltimore, Maryland 21205, USA;
- 4Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA;
- 5Departamento de Biologia General, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil;
- 6RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan;
- 7RIKEN, Preventive Medicine and Diagnostic Innovation Program, Yokohama, 351-0198, Japan;
- 8Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA;
- 9Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA;
- 10Laboratory of Systems Biology and Computational Genetics, VIGG RAS, 117971 Moscow, Russia
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↵11 These authors contributed equally to this work.
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 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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.254656.119.
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Freely available online through the Genome Research Open Access option.
- Received July 12, 2019.
- Accepted February 11, 2020.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
