Zacher, Benedikt, Michel, Margaux, Schwalb, Bjoern, Cramer, Patrick, Tresch, Achim and Gagneur, Julien ORCID: 0000-0002-8924-8365 (2017). Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN. PLoS One, 12 (1). SAN FRANCISCO: PUBLIC LIBRARY SCIENCE. ISSN 1932-6203

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Abstract

Accurate maps of promoters and enhancers are required for understanding transcriptional regulation. Promoters and enhancers are usually mapped by integration of chromatin assays charting histone modifications, DNA accessibility, and transcription factor binding. However, current algorithms are limited by unrealistic data distribution assumptions. Here we propose GenoSTAN (Genomic STate ANnotation), a hidden Markov model overcoming these limitations. We map promoters and enhancers for 127 cell types and tissues from the ENCODE and Roadmap Epigenomics projects, today's largest compendium of chromatin assays. Extensive benchmarks demonstrate that GenoSTAN generally identifies promoters and enhancers with significantly higher accuracy than previous methods. Moreover, GenoSTAN-derived promoters and enhancers showed significantly higher enrichment of complex trait-associated genetic variants than current annotations. Altogether, GenoSTAN provides an easy-to-use tool to define promoters and enhancers in any system, and our annotation of human transcriptional cis-regulatory elements constitutes a rich resource for future research in biology and medicine.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Zacher, BenediktUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Michel, MargauxUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Schwalb, BjoernUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Cramer, PatrickUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Tresch, AchimUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Gagneur, JulienUNSPECIFIEDorcid.org/0000-0002-8924-8365UNSPECIFIED
URN: urn:nbn:de:hbz:38-242784
DOI: 10.1371/journal.pone.0169249
Journal or Publication Title: PLoS One
Volume: 12
Number: 1
Date: 2017
Publisher: PUBLIC LIBRARY SCIENCE
Place of Publication: SAN FRANCISCO
ISSN: 1932-6203
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
HIDDEN MARKOV-MODELS; HUMAN GENOME; CHROMATIN-STATE; SYSTEMATIC ANNOTATION; REGULATORY MOTIFS; HOT REGIONS; TRANSCRIPTION; DISCOVERY; ELEMENTS; DISTINCTMultiple languages
Multidisciplinary SciencesMultiple languages
Refereed: Yes
URI: http://kups.ub.uni-koeln.de/id/eprint/24278

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