refTSS: A Reference Data Set for Human and Mouse Transcription Start Sites

被引：60

作者：

Abugessaisa, Imad ^{[1
]}

Noguchi, Shuhei ^{[1
]}

Hasegawa, Akira ^{[1
]}

Kondo, Atsushi ^{[1
]}

Kawaji, Hideya ^{[1
,2
]}

Carninci, Piero ^{[1
]}

Kasukawa, Takeya ^{[1
]}

机构：

[1] RIKEN, Ctr Integrat Med Sci, Tsurumi Ku, 1-7-22 Suehiro Cho, Yokohama, Kanagawa 2300045, Japan

[2] RIKEN, Prevent Med & Diag Innovat Program, 2-1 Hirosawa, Wako, Saitama 3510198, Japan

来源：

JOURNAL OF MOLECULAR BIOLOGY | 2019年 / 431卷 / 13期

关键词：

transcription start sites; transcriptional regulation; data integration; annotation; reference data; NONCODING RNAS; GENOME; ELEMENTS; ANNOTATION; EXPRESSION; ENHANCERS; ATLAS;

D O I：

10.1016/j.jmb.2019.04.045

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Transcription starts at genomic positions called transcription start sites (TSSs), producing RNAs, and is mainly regulated by genomic elements and transcription factors binding around these TSSs. This indicates that TSSs may be a better unit to integrate various data sources related to transcriptional events, including regulation and production of RNAs. However, although several TSS datasets and promoter atlases are available, a comprehensive reference set that integrates all known TSSs is lacking. Thus, we constructed a reference dataset of TSSs (refTSS) for the human and mouse genomes by collecting publicly available TSS annotations and promoter resources, such as FANTOM5, DBTSS, EPDnew, and ENCODE. The data set consists of genomic coordinates of TSS peaks, their gene annotations, quality check results, and conservation between human and mouse. We also developed a web interface to browse the refTSS (http://reftss.clst.riken.jp/). Users can access the resource for collecting and integrating data and information about transcriptional regulation and transcription products. (C) 2019 The Authors. Published by Elsevier Ltd.

引用

页码：2407 / 2422

页数：16

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