東北大学研究者紹介

所属学協会 1

日本バイオインフォマティクス学会

2024年～継続中

研究分野 1

情報通信 / 生命、健康、医療情報学 /

論文 10

C4S DB: Comprehensive Collection and Comparison for ChIP-Seq Database

Hayato Anzawa, Kengo Kinoshita

Journal of Molecular Biology　435　(14)　168157-168157　2023年7月24日
出版者・発行元： Elsevier {BV}
DOI： 10.1016/j.jmb.2023.168157 　

ISSN：0022-2836
Theoretical characterisation of strand cross-correlation in ChIP-seq 国際誌査読有り

Hayato Anzawa, Hitoshi Yamagata, Kengo Kinoshita

BMC Bioinformatics　21　(1)　2020年7月24日
出版者・発行元： Springer Science and Business Media LLC
DOI： 10.21203/rs.2.16602/v3 　

ISSN：1471-2105

eISSN：1471-2105

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Abstract Background Strand cross-correlation profiles are used for both peak calling pre-analysis and quality control (QC) in chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis. Despite its potential for robust and accurate assessments of signal-to-noise ratio (S/N) because of its peak calling independence, it remains unclear what aspects of quality such strand cross-correlation profiles actually measure. Results We introduced a simple model to simulate the mapped read-density of ChIP-seq and then derived the theoretical maximum and minimum of cross-correlation coefficients between strands. The results suggest that the maximum coefficient of typical ChIP-seq samples is directly proportional to the number of total mapped reads and the square of the ratio of signal reads, and inversely proportional to the number of peaks and the length of read-enriched regions. Simulation analysis supported our results and evaluation using 790 ChIP-seq data obtained from the public database demonstrated high consistency between calculated cross-correlation coefficients and estimated coefficients based on the theoretical relations and peak calling results. In addition, we found that the mappability-bias-correction improved sensitivity, enabling differentiation of maximum coefficients from the noise level. Based on these insights, we proposed virtual S/N (VSN), a novel peak call-free metric for S/N assessment. We also developed PyMaSC, a tool to calculate strand cross-correlation and VSN efficiently. VSN achieved most consistent S/N estimation for various ChIP targets and sequencing read depths. Furthermore, we demonstrated that a combination of VSN and pre-existing peak calling results enable the estimation of the numbers of detectable peaks for posterior experiments and assess peak calling results. Conclusions We present the first theoretical insights into the strand cross-correlation, and the results reveal the potential and the limitations of strand cross-correlation analysis. Our quality assessment framework using VSN provides peak call-independent QC and will help in the evaluation of peak call analysis in ChIP-seq experiments.
PNPO–PLP axis senses prolonged hypoxia in macrophages by regulating lysosomal activity

Hiroki Sekine, Haruna Takeda, Norihiko Takeda, Akihiro Kishino, Hayato Anzawa, Takayuki Isagawa, Nao Ohta, Shohei Murakami, Hideya Iwaki, Nobufumi Kato, Shu Kimura, Zun Liu, Koichiro Kato, Fumiki Katsuoka, Masayuki Yamamoto, Fumihito Miura, Takashi Ito, Masatomo Takahashi, Yoshihiro Izumi, Hiroyuki Fujita, Hitoshi Yamagata, Takeshi Bamba, Takaaki Akaike, Norio Suzuki, Kengo Kinoshita, Hozumi Motohashi

Nature Metabolism　2024年5月31日
出版者・発行元： Springer Science and Business Media LLC
DOI： 10.1038/s42255-024-01053-4 　

eISSN：2522-5812
Whole blood transcriptome analysis for age- and gender-specific gene expression profiling in Japanese individuals

Yu-ichi Aoki, Keiko Taguchi, Hayato Anzawa, Junko Kawashima, Noriko Ishida, Akihito Otsuki, Atsushi Hasegawa, Liam Baird, Takafumi Suzuki, Ikuko N Motoike, Kinuko Ohneda, Kazuki Kumada, Fumiki Katsuoka, Kengo Kinoshita, Masayuki Yamamoto

The Journal of Biochemistry　2024年5月31日

DOI： 10.1093/jb/mvae008 　
Identifying key genes in COPD risk via multiple population data integration and gene prioritization. 国際誌

Afeefa Zainab, Hayato Anzawa, Kengo Kinoshita

PloS one　19　(11)　e0305803　2024年

DOI： 10.1371/journal.pone.0305803 　

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Chronic obstructive pulmonary disease (COPD) is a highly prevalent disease, making it a leading cause of death worldwide. Several genome-wide association studies (GWAS) have been conducted to identify loci associated with COPD. However, different ancestral genetic compositions for the same disease across various populations present challenges in studies involving multi-population data. In this study, we aimed to identify protein-coding genes associated with COPD by prioritizing genes for each population's GWAS data, and then combining these results instead of performing a common meta-GWAS due to significant sample differences in different population cohorts. Lung function measurements are often used as indicators for COPD risk prediction; therefore, we used lung function GWAS data from two populations, Japanese and European, and re-evaluated them using a multi-population gene prioritization approach. This study identified significant single nucleotide variants (SNPs) in both Japanese and European populations. The Japanese GWAS revealed nine significant SNPs and four lead SNPs in three genomic risk loci. In comparison, the European population showed five lead SNPs and 17 independent significant SNPs in 21 genomic risk loci. A comparative analysis of the results found 28 similar genes in the prioritized gene lists of both populations. We also performed a standard meta-analysis for comparison and identified 18 common genes in both populations. Our approach demonstrated that trans-ethnic linkage disequilibrium (LD) could detect some significant novel associations and genes that have yet to be reported or were missed in previous analyses. The study suggests that a gene prioritization approach for multi-population analysis using GWAS data may be a feasible method to identify new associations in data with genetic diversity across different populations. It also highlights the possibility of identifying generalized and population-specific treatment and diagnostic options.
Deficiency of CHAMP1, a gene related to intellectual disability, causes impaired neuronal development and a mild behavioural phenotype 査読有り

Masayoshi Nagai, Kenji Iemura, Takako Kikkawa, Sharmin Naher, Satoko Hattori, Hideo Hagihara, Koh-ichi Nagata, Hayato Anzawa, Risa Kugisaki, Hideki Wanibuchi, Takaya Abe, Kenichi Inoue, Kengo Kinoshita, Tsuyoshi Miyakawa, Noriko Osumi, Kozo Tanaka

Brain Communications　4　(5)　2022年9月1日
出版者・発行元： Oxford University Press ({OUP})
DOI： 10.1093/braincomms/fcac220 　

ISSN：2632-1297

eISSN：2632-1297
High levels of chromosomal instability facilitate the tumor growth and sphere formation 査読有り

Iemura, K., Anzawa, H., Funayama, R., Iwakami, R., Nakayama, K., Kinoshita, K., Tanaka, K.

Cancer Science　113　(8)　2727-2737　2022年6月5日
出版者・発行元： Wiley
DOI： 10.1111/cas.15457 　

ISSN：1349-7006 1347-9032

eISSN：1349-7006
CEBPB is required for NRF2-mediated drug resistance in NRF2-activated non-small cell lung cancer cells 査読有り

Okazaki, K., Anzawa, H., Katsuoka, F., Kinoshita, K., Sekine, H., Motohashi, H.

Journal of Biochemistry　171　(5)　567-578　2022年2月7日
出版者・発行元： Oxford University Press ({OUP})
DOI： 10.1093/jb/mvac013 　

ISSN：1756-2651 0021-924X

eISSN：1756-2651
Enhancer remodeling promotes tumor-initiating activity in NRF2-activated non-small cell lung cancers 査読有り

Keito Okazaki, Hayato Anzawa, Zun Liu, Nao Ota, Hiroshi Kitamura, Yoshiaki Onodera, Md. Morshedul Alam, Daisuke Matsumaru, Takuma Suzuki, Fumiki Katsuoka, Shu Tadaka, Ikuko Motoike, Mika Watanabe, Kazuki Hayasaka, Akira Sakurada, Yoshinori Okada, Masayuki Yamamoto, Takashi Suzuki, Kengo Kinoshita, Hiroki Sekine, Hozumi Motohashi

Nature Communications　11　(1)　2020年11月20日
出版者・発行元： Springer Science and Business Media LLC
DOI： 10.1038/s41467-020-19593-0 　

ISSN：2041-1723

eISSN：2041-1723
Landscape of electrophilic and inflammatory stress-mediated gene regulation in human lymphoblastoid cell lines 査読有り

Noriko Ishida, Yuichi Aoki, Fumiki Katsuoka, Ichiko Nishijima, Takahiro Nobukuni, Hayato Anzawa, Li Bin, Miyuki Tsuda, Kazuki Kumada, Hisaaki Kudo, Takahiro Terakawa, Akihito Otsuki, Kengo Kinoshita, Riu Yamashita, Naoko Minegishi, Masayuki Yamamoto

Free Radical Biology and Medicine　161　71-83　2020年10月2日
出版者・発行元： Elsevier {BV}
DOI： 10.1016/j.freeradbiomed.2020.09.023 　

ISSN：0891-5849

︎全件表示 ︎最初の5件までを表示

MISC 2

東北メディカル・メガバンク計画健康調査における中心角膜厚のゲノムワイド関連解析

布施昇男, 安澤隼人, 元池育子, 櫻井美由紀, 木下賢吾, 山本雅之

日本眼科学会雑誌　128　2024年

ISSN： 0029-0203
転写因子NRF2の持続的活性化によるエンハンサーリモデリングと腫瘍幹細胞性の増強

岡崎慶斗, 安澤隼人, 岡田克典, 鈴木貴, 木下賢吾, 関根弘樹, 本橋ほづみ

日本生化学会大会(Web)　94th　2021年

講演・口頭発表等 5

C4S DB: Comprehensive Collection and Comparison for ChIP-Seq Database

Hayato Anzawa, Kengo Kinoshita

1st Asia & Paciﬁc Bioinformatics Joint Conference (APBJC 2024)　2024年10月23日
Large-scale assessment of ChIP-seq quality metrics toward peak call-free quality control

Hayato Anzawa, Kengo Kinoshita

29th Conference on Intelligent Systems for Molecular Biology and the 20th European Conference on Computational Biology　2021年7月27日
Theoretical estimation of the strand cross-correlation in ChIP-Seq data

Hayato Anzawa, Hitoshi Yamagata, Kengo Kinoshita

Intelligent Systems for Molecular Biology and European Conference on Computational Biology, 2019　2019年7月22日
ChIP-Seqデータのクラスタリングによる実験条件・解析手法に起因するバイアスの可視化

安澤隼人, 木下賢吾

NGS現場の会第五回研究会　2017年5月22日
Model based discrimination method of ChIPed data from control data in ChIP-seq experiment dataset

Hayato Anzawa, Kengo Kinoshita

Informatics In Biology, Medicine and Pharmacology 2016　2016年9月30日

共同研究・競争的資金等の研究課題 1

逐次更新を実現する二次データベース構築手法の開発とレギュロームデータへの適用

安澤隼人

提供機関：Japan Society for the Promotion of Science

制度名：Grants-in-Aid for Scientific Research

研究種目：Grant-in-Aid for Early-Career Scientists

研究機関：Tohoku University

2024年4月1日～ 2027年3月31日

担当経験のある科目(授業) 4

プログラミング演習A　東北大学学部専門科目
創造工学研修　東北大学学部専門科目
生命情報システム科学　東北大学大学院専門科目
電気・通信・電子・情報工学実験C　東北大学学部専門科目