Gateways to the FANTOM5 promoter level mammalian expression atlas

Lizio, Marina; Harshbarger, Jayson; Shimoji, Hisashi; Severin, Jessica; Kasukawa, Takeya; Sahin, Serkan; Abugessaisa, Imad; Fukuda, Shiro; Hori, Fumi; Ishikawa-Kato, Sachi; Mungall, Christopher J.; Arner, Erik; Baillie, J. Kenneth; Bertin, Nicolas; Bono, Hidemasa; de Hoon, Michiel; Diehl, Alexander D.; Dimont, Emmanuel; Freeman, Tom C.; Fujieda, Kaori; Hide, Winston; Kaliyaperumal, Rajaram; Katayama, Toshiaki; Lassmann, Timo; Meehan, Terrence F.; Nishikata, Koro; Ono, Hiromasa; Rehli, Michael; Sandelin, Albin; Schultes, Erik A.; ‘t Hoen, Peter A. C.; Tatum, Zuotian; Thompson, Mark; Toyoda, Tetsuro; Wright, Derek W.; Daub, Carsten O.; Itoh, Masayoshi; Carninci, Piero; Hayashizaki, Yoshihide; Forrest, Alistair R. R.; Kawaji, Hideya

doi:10.1186/s13059-014-0560-6

Title: Gateways to the FANTOM5 promoter level mammalian expression atlas

Journal Article · Mon Jan 05 00:00:00 EST 2015 · GenomeBiology.com

DOI:https://doi.org/10.1186/s13059-014-0560-6· OSTI ID:1256488

Lizio, Marina ^[1]; Harshbarger, Jayson ^[1]; Shimoji, Hisashi ^[1]; Severin, Jessica ^[1]; Kasukawa, Takeya ^[2]; Sahin, Serkan ^[1]; Abugessaisa, Imad ^[2]; Fukuda, Shiro ^[3]; Hori, Fumi ^[1]; Ishikawa-Kato, Sachi ^[1]; Mungall, Christopher J. ^[4]; Arner, Erik ^[1]; Baillie, J. Kenneth ^[5]; Bertin, Nicolas ^[6]; Bono, Hidemasa ^[7]; de Hoon, Michiel ^[1]; Diehl, Alexander D. ^[8]; Dimont, Emmanuel ^[9]; Freeman, Tom C. ^[5]; Fujieda, Kaori ^[7] more »

RIKEN Yokohama Institute, Kanagawa (Japan); RIKEN Center for Life Science Technologie, Kanagawa (Japan)
RIKEN Center for Life Science Technologie, Kanagawa (Japan)
RIKEN Yokohama Institute, Kanagawa (Japan)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Univ. of Edinburgh, Scotland (United Kingdom)
RIKEN Yokohama Institute, Kanagawa (Japan); RIKEN Center for Life Science Technologie, Kanagawa (Japan); National Univ. of Singapore (Singapore)
Research Organization of Information Systems, Chiba (Japan)
Univ. at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY (United States)
Harvard School of Public Health, Boston, MA (United States)
Harvard School of Public Health, Boston, MA (United States); Univ. of Sheffield, Sheffield (United Kingdom)
Leiden Univ. Medical Center, Leiden (Netherlands)
RIKEN Yokohama Institute, Kanagawa (Japan); RIKEN Center for Life Science Technologie, Kanagawa (Japan); The Univ. of Western Australia, Western Australia (Australia)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge (United Kingdom)
RIKEN Advanced Center for Computing and Communication, Saitama (Japan)
Univ. Hospital Regensburg, Regensburg (Germany)
Copenhagen Univ., Copenhagen (Denmark)
Leiden Univ. Medical Center, Leiden (Netherlands); Leiden Univ., Leiden (Netherlands)
RIKEN Yokohama Institute, Kanagawa (Japan); RIKEN Center for Life Science Technologie, Kanagawa (Japan); RIKEN Preventive Medicine and Diagnosis Innovative Program, Saitama (Japan)
RIKEN Yokohama Institute, Kanagawa (Japan); RIKEN Preventive Medicine and Diagnosis Innovative Program, Saitama (Japan)
RIKEN Yokohama Institute, Kanagawa (Japan); RIKEN Center for Life Science Technologie, Kanagawa (Japan); RIKEN Preventive Medicine and Diagnosis Innovative Program, Saitama (Japan); RIKEN Advanced Center for Computing and Communication, Saitama (Japan)

The FANTOM5 project investigates transcription initiation activities in more than 1,000 human and mouse primary cells, cell lines and tissues using CAGE. Based on manual curation of sample information and development of an ontology for sample classification, we assemble the resulting data into a centralized data resource (http://fantom.gsc.riken.jp/5/). In conclusion, this resource contains web-based tools and data-access points for the research community to search and extract data related to samples, genes, promoter activities, transcription factors and enhancers across the FANTOM5 atlas.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Contributing Organization:: The FANTOM consortium

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1256488

Journal Information:: GenomeBiology.com, Vol. 16, Issue 1; ISSN 1465-6906

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 485 works

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Maintenance of active chromatin states by HMGN2 is required for stem cell identity in a pluripotent stem cell model Garza-Manero, Sylvia; Sindi, Abdulmajeed Abdulghani A.; Mohan, Gokula Epigenetics & Chromatin, Vol. 12, Issue 1 https://doi.org/10.1186/s13072-019-0320-7	journal	December 2019
ATP6V0d2 controls Leishmania parasitophorous vacuole biogenesis via cholesterol homeostasis Pessoa, Carina Carraro; Reis, Luiza Campos; Ramos-Sanchez, Eduardo Milton PLOS Pathogens, Vol. 15, Issue 6 https://doi.org/10.1371/journal.ppat.1007834	journal	June 2019
CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness. Morgan, Michael; Marioni, John Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.27259	text	January 2018
Hepatocyte gene expression and DNA methylation as ancestry-dependent mechanisms in African Americans Park, C. S.; De, T.; Xu, Y. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.60375	text	January 2019
Hexosamine Biosynthetic Pathway and Glycosylation Regulate Cell Migration in Melanoma Cells de Queiroz, Rafaela Muniz; Oliveira, Isadora Araújo; Piva, Bruno Frontiers in Oncology, Vol. 9 https://doi.org/10.3389/fonc.2019.00116	journal	March 2019
Timing and localization of human dystrophin isoform expression provide insights into the cognitive phenotype of Duchenne muscular dystrophy Doorenweerd, N.; Mahfouz, A.; van Putten, M. Neuromuscular Disorders, Vol. 27 https://doi.org/10.1016/j.nmd.2017.06.087	journal	October 2017
Identifying noncoding risk variants using disease-relevant gene regulatory networks Gao, Long; Uzun, Yasin; Gao, Peng Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-03133-y	journal	February 2018
The genetics of obstructive sleep apnoea Kent, Brian D.; Ryan, Silke; McNicholas, Walter T. Current Opinion in Pulmonary Medicine, Vol. 16, Issue 6 https://doi.org/10.1097/mcp.0b013e32833ef7fe	journal	January 2010
A widespread role for SLC transmembrane transporters in resistance to cytotoxic drugs Girardi, Enrico; César-Razquin, Adrián; Papakostas, Konstantinos Nature Chemical Biology https://doi.org/10.1101/726539	posted_content	August 2019
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Characterization of the human RFX transcription factor family by regulatory and target gene analysis Sugiaman-Trapman, Debora; Vitezic, Morana; Jouhilahti, Eeva-Mari BMC Genomics, Vol. 19, Issue 1 https://doi.org/10.1186/s12864-018-4564-6	journal	March 2018
Directional association test reveals high-quality putative cancer driver biomarkers including noncoding RNAs Zhong, Hua; Song, Mingzhou BMC Medical Genomics, Vol. 12, Issue S7 https://doi.org/10.1186/s12920-019-0565-9	journal	December 2019
Comprehensive genomic analysis reveals dynamic evolution of endogenous retroviruses that code for retroviral-like protein domains Ueda, Mahoko Takahashi; Kryukov, Kirill; Mitsuhashi, Satomi Mobile DNA, Vol. 11, Issue 1 https://doi.org/10.1186/s13100-020-00224-w	journal	September 2020
FANTOM5 CAGE profiles of human and mouse samples Noguchi, Shuhei; Arakawa, Takahiro; Fukuda, Shiro Charité - Universitätsmedizin Berlin https://doi.org/10.17169/refubium-24538	text	January 2017
Long noncoding RNA expression profiling in cancer: Challenges and opportunities Lorenzi, Lucía; Avila Cobos, Francisco; Decock, Anneleen Genes, Chromosomes and Cancer, Vol. 58, Issue 4 https://doi.org/10.1002/gcc.22709	journal	January 2019
Transcriptomic and open chromatin atlas of high-resolution anatomical regions in the rhesus macaque brain Yin, Senlin; Lu, Keying; Tan, Tao Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-14368-z	journal	January 2020
Timing and localization of human dystrophin isoform expression provide insights into the cognitive phenotype of Duchenne muscular dystrophy Doorenweerd, Nathalie; Mahfouz, Ahmed; van Putten, Maaike Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-12981-5	journal	October 2017
Repression of ferritin light chain translation by human eIF3 Pulos-Holmes, Mia C.; Srole, Daniel N.; Lee, Amy S. Y. eLife https://doi.org/10.1101/316299	journal	May 2019
Multiplexed dissection of a model human transcription factor binding site architecture Davis, Jessica E.; Insigne, Kimberly D.; Jones, Eric M. BioRxiv https://doi.org/10.1101/625434	posted_content	May 2019
xCell: digitally portraying the tissue cellular heterogeneity landscape Aran, Dvir; Hu, Zicheng; Butte, Atul J. Genome Biology, Vol. 18, Issue 1 https://doi.org/10.1186/s13059-017-1349-1	journal	November 2017
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The Stk35 locus contributes to normal gametogenesis and encodes a lncRNA responsive to oxidative stress Miyamoto, Yoichi; Whiley, Penny A. F.; Goh, Hoey Y. Biology Open https://doi.org/10.1242/bio.032631	journal	January 2018
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The BioMart community portal: an innovative alternative to large, centralized data repositories. Smedley, Damian; Haider, Syed; Durinck, Steffen Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.57576	text	January 2015
Generation of Retinaldehyde for Retinoic Acid Biosynthesis Belyaeva, Olga V.; Adams, Mark K.; Popov, Kirill M. Biomolecules https://doi.org/10.20944/preprints201912.0211.v1	journal	December 2019
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The adaptor protein ARA55 and the nuclear kinase HIPK1 assist c-Myb in recruiting p300 to chromatin Bengtsen, Mads; Sørensen, Linda; Aabel, Linn Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Vol. 1860, Issue 7 https://doi.org/10.1016/j.bbagrm.2017.05.001	journal	July 2017
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RNA damage in biological conflicts and the diversity of responding RNA repair systems Burroughs, A. Maxwell; Aravind, L. Nucleic Acids Research, Vol. 44, Issue 18 https://doi.org/10.1093/nar/gkw722	journal	August 2016
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Update of the FANTOM web resource: expansion to provide additional transcriptome atlases Lizio, Marina; Abugessaisa, Imad; Noguchi, Shuhei Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1099	journal	November 2018
Juxtacap Nucleotide Sequence Modulates eIF4E Binding and Translation Keys, Heather R.; Sabatini, David M. BioRxiv https://doi.org/10.1101/165142	posted_content	July 2017
dyngen: a multi-modal simulator for spearheading new single-cell omics analyses Cannoodt, Robrecht; Saelens, Wouter; Deconinck, Louise Nature Communications https://doi.org/10.1101/2020.02.06.936971	journal	September 2020
Cellular response to small molecules that selectively stall protein synthesis by the ribosome Liaud, Nadege; Horlbeck, Max A.; Gilbert, Luke A. PLOS Genetics https://doi.org/10.1101/461624	posted_content	November 2018
Analysis of regulatory element evolution between human and mouse reveals a lack of cis-trans compensation Mattioli, Kaia; Oliveros, Winona; Gerhardinger, Chiara https://doi.org/10.1101/847491	preprint	November 2019
Type VII Collagen in the Human Accommodation System: Expression in Ciliary Body, Zonules, and Lens Capsule Wullink, Bart; Pas, Hendri H.; Van der Worp, Roelofje J. Investigative Opthalmology & Visual Science, Vol. 59, Issue 2 https://doi.org/10.1167/iovs.17-23425	journal	February 2018
Systematic analysis of transcription start sites in avian development Lizio, Marina; Deviatiiarov, Ruslan; Nagai, Hiroki PLOS Biology, Vol. 15, Issue 9 https://doi.org/10.1371/journal.pbio.2002887	journal	September 2017
metagene Profiles Analyses Reveal Regulatory Element’s Factor-Specific Recruitment Patterns Joly Beauparlant, Charles; Lamaze, Fabien C.; Deschênes, Astrid PLOS Computational Biology, Vol. 12, Issue 8 https://doi.org/10.1371/journal.pcbi.1004751	journal	August 2016
RATA: A method for high-throughput identification of RNA bound transcription factors. Schmidt, Karyn; Buquicchio, Frank; Carroll, Johanna S. Journal of Biological Methods https://doi.org/10.17863/cam.39227	journalarticle	January 2017
The relationships among bovine αS-casein phosphorylation isoforms suggest different phosphorylation pathways Fang, Z. H.; Visker, M. H. P. W.; Miranda, G. Journal of Dairy Science, Vol. 99, Issue 10 https://doi.org/10.3168/jds.2016-11250	journal	October 2016
Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line Lizio, Marina; Ishizu, Yuri; Itoh, Masayoshi Frontiers in Genetics, Vol. 6 https://doi.org/10.3389/fgene.2015.00331	journal	November 2015
HMGA2 Antisense Long Non-coding RNAs as New Players in the Regulation of HMGA2 Expression and Pancreatic Cancer Promotion Ros, Gloria; Pegoraro, Silvia; De Angelis, Paolo Frontiers in Oncology, Vol. 9 https://doi.org/10.3389/fonc.2019.01526	journal	January 2020
Epigenome Aberrations: Emerging Driving Factors of the Clear Cell Renal Cell Carcinoma Mehdi, Ali; Riazalhosseini, Yasser International Journal of Molecular Sciences, Vol. 18, Issue 8 https://doi.org/10.3390/ijms18081774	journal	August 2017
Computational analysis of brain transcriptome atlases Mahfouz, A. M. E. T. A. Delft University of Technology https://doi.org/10.4233/uuid:e8241c58-a443-46b7-8e98-c91078d338df	text	January 2016

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