DBTSS/DBKERO for integrated analysis of transcriptional regulation

Ayako Suzuki, Shin Kawano, Toutai Mitsuyama, Mikita Suyama, Yae Kanai, Katsuhiko Shirahige, Hiroyuki Sasaki, Katsushi Tokunaga, Katsuya Tsuchihara, Sumio Sugano, Kenta Nakai, Yutaka Suzuki

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

DBTSS (Database of Transcriptional Start Sites)/DBKERO (Database of Kashiwa Encyclopedia for human genome mutations in Regulatory regions and their Omics contexts) is the database originally initiated with the information of transcriptional start sites and their upstream transcriptional regulatory regions. In recent years, we updated the database to assist users to elucidate biological relevance of the human genome variations or somatic mutations in cancers which may affect the transcriptional regulation. In this update, we facilitate interpretations of disease associated genomic variation, using the Japanese population as a model case. We enriched the genomic variation dataset consisting of the 13,368 individuals collected for various genome-wide association studies and the reference epigenome information in the surrounding regions using a total of 455 epigenome datasets (four tissue types from 67 healthy individuals) collected for the International Human Epigenome Consortium (IHEC). The data directly obtained from the clinical samples was associated with that obtained from various model systems, such as the drug perturbation datasets using cultured cancer cells. Furthermore, we incorporated the results obtained using the newly developed analytical methods, Nanopore/10x Genomics long-read sequencing of the human genome and single cell analyses. The database is made publicly accessible at the URL (http://dbtss.hgc.jp/).

Original languageEnglish
Pages (from-to)D229-D238
JournalNucleic Acids Research
Volume46
Issue numberD1
DOIs
Publication statusPublished - 2018 Jan 1

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Databases
Human Genome
Nucleic Acid Regulatory Sequences
Nanopores
Encyclopedias
Single-Cell Analysis
Mutation
Genome-Wide Association Study
Genomics
Cultured Cells
Neoplasms
Pharmaceutical Preparations
Population
Datasets

ASJC Scopus subject areas

  • Genetics

Cite this

Suzuki, A., Kawano, S., Mitsuyama, T., Suyama, M., Kanai, Y., Shirahige, K., ... Suzuki, Y. (2018). DBTSS/DBKERO for integrated analysis of transcriptional regulation. Nucleic Acids Research, 46(D1), D229-D238. https://doi.org/10.1093/nar/gkx1001

DBTSS/DBKERO for integrated analysis of transcriptional regulation. / Suzuki, Ayako; Kawano, Shin; Mitsuyama, Toutai; Suyama, Mikita; Kanai, Yae; Shirahige, Katsuhiko; Sasaki, Hiroyuki; Tokunaga, Katsushi; Tsuchihara, Katsuya; Sugano, Sumio; Nakai, Kenta; Suzuki, Yutaka.

In: Nucleic Acids Research, Vol. 46, No. D1, 01.01.2018, p. D229-D238.

Research output: Contribution to journalArticle

Suzuki, A, Kawano, S, Mitsuyama, T, Suyama, M, Kanai, Y, Shirahige, K, Sasaki, H, Tokunaga, K, Tsuchihara, K, Sugano, S, Nakai, K & Suzuki, Y 2018, 'DBTSS/DBKERO for integrated analysis of transcriptional regulation', Nucleic Acids Research, vol. 46, no. D1, pp. D229-D238. https://doi.org/10.1093/nar/gkx1001
Suzuki A, Kawano S, Mitsuyama T, Suyama M, Kanai Y, Shirahige K et al. DBTSS/DBKERO for integrated analysis of transcriptional regulation. Nucleic Acids Research. 2018 Jan 1;46(D1):D229-D238. https://doi.org/10.1093/nar/gkx1001
Suzuki, Ayako ; Kawano, Shin ; Mitsuyama, Toutai ; Suyama, Mikita ; Kanai, Yae ; Shirahige, Katsuhiko ; Sasaki, Hiroyuki ; Tokunaga, Katsushi ; Tsuchihara, Katsuya ; Sugano, Sumio ; Nakai, Kenta ; Suzuki, Yutaka. / DBTSS/DBKERO for integrated analysis of transcriptional regulation. In: Nucleic Acids Research. 2018 ; Vol. 46, No. D1. pp. D229-D238.
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