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Recounting the FANTOM Cage Associated Transcriptome

View ORCID ProfileEddie-Luidy Imada, View ORCID ProfileDiego Fernando Sanchez, View ORCID ProfileLeonardo Collado-Torres, Christopher Wilks, Tejasvi Matam, View ORCID ProfileWikum Dinalankara, Aleksey Stupnikov, View ORCID ProfileFrancisco 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, View ORCID ProfilePiero Carninci, FANTOM consortium, View ORCID ProfileAndrew E Jaffe, View ORCID ProfileJeffrey T Leek, View ORCID ProfileAlexander Favorov, View ORCID ProfileGloria R Franco, View ORCID ProfileBen Langmead, View ORCID ProfileLuigi Marchionni
doi: https://doi.org/10.1101/659490
Eddie-Luidy Imada
1Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
2Departamento de Bioquímica e Imunologia, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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Diego Fernando Sanchez
1Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Leonardo Collado-Torres
3Lieber Institute for Brain Development, Baltimore, MD, USA
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Christopher Wilks
4Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
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Tejasvi Matam
1Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Wikum Dinalankara
1Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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  • ORCID record for Wikum Dinalankara
Aleksey Stupnikov
1Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Francisco Lobo-Pereira
5Departamento de Biologia General, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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Chi-Wai Yip
6RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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Kayoko Yasuzawa
6RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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Naoto Kondo
6RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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Masayoshi Itoh
7RIKEN, Preventive Medicine and Diagnostic Innovation Program, Yokohama, Japan
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Harukazu Suzuki
6RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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Takeya Kasukawa
6RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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Chung-Chau Hon
6RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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Michiel JL de Hoon
6RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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Jay W Shin
6RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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Piero Carninci
6RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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Andrew E Jaffe
3Lieber Institute for Brain Development, Baltimore, MD, USA
8Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
9Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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Jeffrey T Leek
9Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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Alexander Favorov
1Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
10Laboratory of Systems Biology and Computational Genetics, VIGG RAS, Moscow, RF
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Gloria R Franco
2Departamento de Bioquímica e Imunologia, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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Ben Langmead
4Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
9Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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Luigi Marchionni
1Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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  • For correspondence: marchion@jhu.edu
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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.

Footnotes

  • We added all funding sources.

  • http://marchionnilab.org/fcr2.html

  • https://jhubiostatistics.shinyapps.io/recount/

  • https://github.com/eddieimada/fcr2

  • https://github.com/LieberInstitute/marchionni_projects

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted July 08, 2019.
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Recounting the FANTOM Cage Associated Transcriptome
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, FANTOM consortium, Andrew E Jaffe, Jeffrey T Leek, Alexander Favorov, Gloria R Franco, Ben Langmead, Luigi Marchionni
bioRxiv 659490; doi: https://doi.org/10.1101/659490
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Recounting the FANTOM Cage Associated Transcriptome
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, FANTOM consortium, Andrew E Jaffe, Jeffrey T Leek, Alexander Favorov, Gloria R Franco, Ben Langmead, Luigi Marchionni
bioRxiv 659490; doi: https://doi.org/10.1101/659490

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