統合的な転写制御データ基盤の構築

研究課題

体系的番号	JPMJND2202
DOI	https://doi.org/10.52926/JPMJND2202
研究代表者	粕川雄也理化学研究所, 生命医科学研究センター, チームリーダー
研究期間 (年度)	2022 – 2026
概要	転写制御の総合的理解をサポートするため、シスエレメント・トランス因子・エピゲノミクスデータを統合したデータ基盤INTRAREDを構築する。INTRAREDは同一染色体上で遺伝子の発現の調節に関わるゲノム中の領域であるシスエレメントについて、その領域や細胞の種類・状態毎のシスエレメント領域の活性状態を同定して収録したシスエレメントデータベースfanta.bioと、シスエレメントに結合するトランス因子や関連するエピゲノミクス情報を提供するChIP-Atlasで構成され、相互連携したビューを提供する。
研究領域	統合化推進プログラム

報告書

(5件)

2024 中間報告書 ( PDF ) 中間評価書 ( PDF ) 年次報告書 ( PDF )
2023 年次報告書 ( PDF )
2022 年次報告書 ( PDF )

主な研究成果
(18件)

すべて 2024

すべて雑誌論文 (18件) (国際共著 1件、査読あり 6件、オープンアクセス 1件)

[雑誌論文] Update of the FANTOM web resource: enhancement for studying noncoding genomes.2024
- 著者名
  Tomoe Nobusada, Chi Wai Yip, Saumya Agrawal, Jessica Severin, Imad Abugessaisa, Akira Hasegawa, Chung Chau Hon, Satoru Ide, Masaru Koido, Atsushi Kondo, Hiroshi Masuya, Shinya Oki, Michihira Tagami, Toyoyuki Takada, Chikashi Terao, Nishad Thalhath, Scott Walker, Kayoko Yasuzawa, Jay W Shin, Michiel J L de Hoon, Piero Carninci, Hideya Kawaji, Takeya Kasukawa
- 雑誌名
  
  Nucleic acids research
  
  巻: 53 号: D1 ページ: D419-D424
- DOI
  10.1093/nar/gkae1047
- 査読あり / オープンアクセス / 国際共著
[雑誌論文] Extraction of biological terms using large language models enhances the usability of metadata in the BioSample database2024
- 著者名
  Shuya Ikeda, Zhaonan Zou, Hidemasa Bono, Yuki Moriya, Shuichi Kawashima, Toshiaki Katayama, Shinya Oki, Tazro Ohta
- 雑誌名
  
  GigaScience
- DOI
  10.1093/gigascience/giaf070
[雑誌論文] High spatial resolution gene expression profiling and characterization of neuroblasts migrating in the peri-injured cortex using photo-isolation chemistry2024
- 著者名
  Takuya Miyamoto, Kazuya Kuboyama, Mizuki Honda, Yasuyuki Ohkawa, Shinya Oki, Kazunobu Sawamoto
- 雑誌名
  
  Frontiers in Neuroscience
  
  巻: 18
- DOI
  10.3389/fnins.2024.1504047
[雑誌論文] Structural and molecular properties of mumps virus inclusion bodies2024
- 著者名
  Noriyo NAGATA, Tadaki Suzuki, Yasuyuki Ohkawa, Hiroshi Katoh, Kimura Ryuichi, Tsuyoshi Sekizuka, Kohei Matsuoka, Mika Hosogi, Yuki Kitai, Yukiko AKAHORI, Michiyo Kataoka, Hirotaka Kobayashi, Shinya Oki, Makoto Takeda, Fumihiro Kato
- 雑誌名
  
  Science Advances
- DOI
  10.1126/sciadv.adr0359
[雑誌論文] Biallelic null variants in <i>PNPLA8</i> cause microcephaly by reducing the number of basal radial glia2024
- 著者名
  Yuji Nakamura, et al
- 雑誌名
  
  Brain
- DOI
  10.1093/brain/awae185
- 査読あり
[雑誌論文] ChIP-Atlas 3.0: a data-mining suite to explore chromosome architecture together with large-scale regulome data2024
- 著者名
  Zhaonan Zou, Tazro Ohta, Shinya Oki
- 雑誌名
  
  Nucleic Acids Research
  
  巻: 52 号: W1 ページ: W45-W53
- DOI
  10.1093/nar/gkae358
- 査読あり
[雑誌論文] Drug-induced cis-regulatory elements in human hepatocytes affect molecular phenotypes associated with adverse reactions2024
- 著者名
  Saki Gotoh-Saito, Ryoko Wada, Hideya Kawaji
- 雑誌名
  
  Nature communications
  
  巻: 16 号: 1 ページ: 3851-3851
- DOI
  10.1101/2024.07.24.604883
[雑誌論文] Analysis of Functional cis-Regulatory Elements Reveals Novel Transcriptional Regulatory Mechanisms in Gonadal Development.2024
- 著者名
  Shizuka Kirino, Ryuichi Nakagawa, Maki Gau, Kei Takasawa, Yasuhiro Murakawa, Hideya Kawaji, Yoshihide Hayashizaki, Tomohiro Morio, Kenichi Kashimada
- 雑誌名
  
  Sexual development : genetics, molecular biology, evolution, endocrinology, embryology, and pathology of sex determination and differentiation
  
  ページ: 1-13
- DOI
  10.1159/000543594
[雑誌論文] Protocol for direct cDNA cap analysis of gene expression for paired-end patterned flow cell sequencing.2024
- 著者名
  Diane Delobel, Hiromi Nishiyori-Sueki, Ilaria Nisoli, Hideya Kawaji, Pauline Robbe, Piero Carninci, Hazuki Takahashi
- 雑誌名
  
  STAR protocols
  
  巻: 6 号: 1 ページ: 103594-103594
- DOI
  10.1016/j.xpro.2024.103594
[雑誌論文] Tissue degrading and remodelling molecules in giant cell arteritis2024
- 著者名
  Nobumasa Watanabe, Yuichiro Hara, Yasumasa Nishito, Mai Kounoe, Kazunari Sekiyama, Eisuke Takamasu, Takayasu Kise, Naofumi Chinen, Kota Shimada, Makoto Sugihara, Hideya Kawaji
- 雑誌名
  
  Rheumatology
  
  巻: 64 号: 5 ページ: 3095-103
- DOI
  10.1093/rheumatology/keae710
[雑誌論文] Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.2024
- 著者名
  Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark Diekhans, S?lvia Carbonell-Sala, Brian Williams, Jane E Loveland, Maite De Mar?a, Matthew S Adams, Gabriela Balderrama-Gutierrez, Amit K Behera, Jose M Gonzalez Martinez, Toby Hunt, Julien Lagarde, Cindy E Liang, Haoran Li, Marcus Jerryd Meade, David A Moraga Amador, Andrey D Prjibelski, Inanc Birol, Hamed Bostan, Ashley M Brooks, Muhammed Hasan ?elik, Ying Chen, Mei R M Du, Colette Felton, Jonathan G?ke, Saber Hafezqorani, Ralf Herwig, Hideya Kawaji, et al.
- 雑誌名
  
  Nature methods
  
  巻: 21 号: 7 ページ: 1349-1363
- DOI
  10.1038/s41592-024-02298-3
[雑誌論文] An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases.2024
- 著者名
  Akiko Oguchi, Akari Suzuki, Shuichiro Komatsu, Hiroyuki Yoshitomi, Shruti Bhagat, Raku Son, Raoul Jean Pierre Bonnal, Shohei Kojima, Masaru Koido, Kazuhiro Takeuchi, Keiko Myouzen, Gyo Inoue, Tomoya Hirai, Hiromi Sano, Yujiro Takegami, Ai Kanemaru, Itaru Yamaguchi, Yuki Ishikawa, Nao Tanaka, Shigeki Hirabayashi, Riyo Konishi, Sho Sekito, Takahiro Inoue, Juha Kere, Shunichi Takeda, Akifumi Takaori-Kondo, Itaru Endo, Shinpei Kawaoka, Hideya Kawaji, Kazuyoshi Ishigaki, Hideki Ueno, Yoshihide Hayashizaki, Massimiliano Pagani, Piero Carninci, Motoko Yanagita, Nicholas Parrish, Chikashi Terao, Kazuhiko Yamamoto, Yasuhiro Murakawa
- 雑誌名
  
  Science (New York, N.Y.)
  
  巻: 385 号: 6704 ページ: eadd8394
- DOI
  10.1126/science.add8394
[雑誌論文] Systematic Ocular Phenotyping of Knockout Mouse Lines Identifies Genes Associated With Age-Related Corneal Dystrophies.2024
- 著者名
  Andrew Briere, Peter Vo, Benjamin Yang, David Adams, Takanori Amano, Oana Amarie, Zorana Berberovic, Lynette Bower, Steve D M Brown, Samantha Burrill, Soo Young Cho, Sharon Clementson-Mobbs, Abigail D'souza, Mohammad Eskandarian, Ann M Flenniken, Helmut Fuchs, Valerie Gailus-Durner, Yann H?rault, Martin Hrabe de Angelis, Shundan Jin, Russell Joynson, Yeon Kyung Kang, Haerim Kim, Hiroshi Masuya, Hamid Meziane, Ki-Hoan Nam, Hyuna Noh, Lauryl M J Nutter, Marcela Palkova, Jan Prochazka, Miles Joseph Raishbrook, Fabrice Riet, Jason Salazar, Radislav Sedlacek, Mohammed Selloum, Kyoung Yul Seo, Je Kyung Seong, Hae-Sol Shin, Toshihiko Shiroishi, Michelle Stewart, Karen Svenson, Masaru Tamura, Heather Tolentino, Sara Wells, Wolfgang Wurst, Atsushi Yoshiki, Louise Lanoue, K C Kent Lloyd, Brian C Leonard, Michel J Roux, Colin McKerlie, Ala Moshiri
- 雑誌名
  
  Investigative ophthalmology & visual science
  
  巻: 66 号: 5 ページ: 7-7
- DOI
  10.1167/iovs.66.5.7
[雑誌論文] Systematic ocular phenotyping of 8,707 knockout mouse lines identifies genes associated with abnormal corneal phenotypes.2024
- 著者名
  Peter Vo, Denise M Imai-Leonard, Benjamin Yang, Andrew Briere, Andy Shao, M Isabel Casanova, David Adams, Takanori Amano, Oana Amarie, Zorana Berberovic, Lynette Bower, Robert Braun, Steve Brown, Samantha Burrill, Soo Young Cho, Sharon Clementson-Mobbs, Abigail D'Souza, Mary Dickinson, Mohammad Eskandarian, Ann M Flenniken, Helmut Fuchs, Valerie Gailus-Durner, Jason Heaney, Yann H?rault, Martin Hrabe de Angelis, Chih-Wei Hsu, Shundan Jin, Russell Joynson, Yeon Kyung Kang, Haerim Kim, Hiroshi Masuya, Hamid Meziane, Steve Murray, Ki-Hoan Nam, Hyuna Noh, Lauryl M J Nutter, Marcela Palkova, Jan Prochazka, Miles Joseph Raishbrook, Fabrice Riet, Jennifer Ryan, Jason Salazar, Zachery Seavey, John Richard Seavitt, Radislav Sedlacek, Mohammed Selloum, Kyoung Yul Seo, Je Kyung Seong, Hae-Sol Shin, Toshihiko Shiroishi, Michelle Stewart, Karen Svenson, Masaru Tamura, Heather Tolentino, Uchechukwu Udensi, Sara Wells, Jacqueline White, Amelia Willett, Janine Wotton, Wolfgang Wurst, et al.
- 雑誌名
  
  BMC genomics
  
  巻: 26 号: 1 ページ: 48-48
- DOI
  10.1186/s12864-025-11222-8
[雑誌論文] Federated SPARQL query performance evaluation for exploring disease model mouse: combining gene expression, orthology, and disease knowledge graphs.2024
- 著者名
  Tatsuya Kushida, Tarcisio Mendes de Farias, Ana C Sima, Christophe Dessimoz, Hirokazu Chiba, Frederic B Bastian, Hiroshi Masuya
- 雑誌名
  
  BMC medical informatics and decision making
  
  巻: 25 号: Suppl 1 ページ: 189-189
- DOI
  10.1186/s12911-025-03013-8
[雑誌論文] Inference of selective forces on house mouse genomes during secondary contact in East Asia2024
- 著者名
  Fujiwara K, Kubo S, Endo T, Takada T, Shiroishi T, Suzuki H, Osada N
- 雑誌名
  
  Genome Research
  
  巻: 34 号: 3 ページ: 366-375
- DOI
  10.1101/gr.278828.123
- 査読あり
[雑誌論文] Type specimens, taxonomic history, and genetic analysis of the Japanese dancing mouse or waltzer, Mus wagneri variety rotans Droogleever Fortuyn, 1912 (Mammalia, Muridae)2024
- 著者名
  M?nica Cruz, Wim Bergmans, Toyoyuki Takada, Toshihiko Shiroishi, Atsushi Yoshiki
- 雑誌名
  
  ZooKeys
  
  巻: 1200 ページ: 27-39
- DOI
  10.3897/zookeys.1200.118823
- 査読あり
[雑誌論文] HKDC1, a target of TFEB, is essential to maintain both mitochondrial and lysosomal homeostasis, preventing cellular senescence2024
- 著者名
  Cui M, Yamano K, Yamamoto K, Yamamoto-Imoto H, Minami S, Yamamoto T, Matsui S, Kaminishi T, Shima T, Ogura M, Tsuchiya M, Nishino K, Layden BT, Kato H, Ogawa H, Oki S, Okada Y, Isaka Y, Kosako H, Matsuda N, Yoshimori T, Nakamura S
- 雑誌名
  
  Proc Natl Acad Sci USA
  
  巻: 121 号: 2 ページ: e2306454120
- DOI
  10.1073/pnas.2306454120
- 査読あり

統合的な転写制御データ基盤の構築

研究代表者

粕川 雄也 理化学研究所, 生命医科学研究センター, チームリーダー

報告書

主な研究成果

[雑誌論文] Update of the FANTOM web resource: enhancement for studying noncoding genomes.2024

著者名

雑誌名

DOI

[雑誌論文] Extraction of biological terms using large language models enhances the usability of metadata in the BioSample database2024

著者名

雑誌名

DOI

[雑誌論文] High spatial resolution gene expression profiling and characterization of neuroblasts migrating in the peri-injured cortex using photo-isolation chemistry2024

著者名

雑誌名

DOI

[雑誌論文] Structural and molecular properties of mumps virus inclusion bodies2024

著者名

雑誌名

DOI

[雑誌論文] Biallelic null variants in <i>PNPLA8</i> cause microcephaly by reducing the number of basal radial glia2024

著者名

雑誌名

DOI

[雑誌論文] ChIP-Atlas 3.0: a data-mining suite to explore chromosome architecture together with large-scale regulome data2024

著者名

雑誌名

DOI

[雑誌論文] Drug-induced cis-regulatory elements in human hepatocytes affect molecular phenotypes associated with adverse reactions2024

著者名

雑誌名

DOI

[雑誌論文] Analysis of Functional cis-Regulatory Elements Reveals Novel Transcriptional Regulatory Mechanisms in Gonadal Development.2024

著者名

雑誌名

DOI

[雑誌論文] Protocol for direct cDNA cap analysis of gene expression for paired-end patterned flow cell sequencing.2024

著者名

雑誌名

DOI

[雑誌論文] Tissue degrading and remodelling molecules in giant cell arteritis2024

著者名

雑誌名

DOI

[雑誌論文] Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.2024

著者名

雑誌名

DOI

[雑誌論文] An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases.2024

著者名

雑誌名

DOI

[雑誌論文] Systematic Ocular Phenotyping of Knockout Mouse Lines Identifies Genes Associated With Age-Related Corneal Dystrophies.2024

著者名

雑誌名

DOI

[雑誌論文] Systematic ocular phenotyping of 8,707 knockout mouse lines identifies genes associated with abnormal corneal phenotypes.2024

著者名

雑誌名

DOI

[雑誌論文] Federated SPARQL query performance evaluation for exploring disease model mouse: combining gene expression, orthology, and disease knowledge graphs.2024

著者名

雑誌名

DOI

[雑誌論文] Inference of selective forces on house mouse genomes during secondary contact in East Asia2024

著者名

雑誌名

DOI

[雑誌論文] Type specimens, taxonomic history, and genetic analysis of the Japanese dancing mouse or waltzer, Mus wagneri variety rotans Droogleever Fortuyn, 1912 (Mammalia, Muridae)2024

著者名

雑誌名

DOI

[雑誌論文] HKDC1, a target of TFEB, is essential to maintain both mitochondrial and lysosomal homeostasis, preventing cellular senescence2024

著者名

雑誌名

DOI

粕川雄也理化学研究所, 生命医科学研究センター, チームリーダー