التفاصيل البيبلوغرافية
| العنوان: |
RENGE infers gene regulatory networks using time-series single-cell RNA-seq data with CRISPR perturbations |
| المؤلفون: |
Ishikawa, Masato, Sugino, Seiichi, Masuda, Yoshie, Tarumoto, Yusuke, Seto, Yusuke, Taniyama, Nobuko, Wagai, Fumi, Yamauchi, Yuhei, Kojima, Yasuhiro, Kiryu, Hisanori, Yusa, Kosuke, Eiraku, Mototsugu, Mochizuki, Atsushi |
| المساهمون: |
石川, 雅人, 杉野, 成一, 増田, 芳恵, 樽本, 雄介, 瀬戸, 裕介, 谷山, 暢子, 和穎, 文, 山内, 悠平, 小嶋, 泰弘, 木立, 尚孝, 遊佐, 宏介, 永樂, 元次, 望月, 敦史, 70551381 |
| بيانات النشر: |
Springer Nature |
| سنة النشر: |
2023 |
| المجموعة: |
Kyoto University Research Information Repository (KURENAI) / 京都大学学術情報リポジトリ |
| مصطلحات موضوعية: |
Dynamical systems, Gene regulation, Gene regulatory networks, Regulatory networks |
| الوصف: |
摂動に基づく遺伝子制御ネットワーク推定 --数理モデルによる自動決定--. 京都大学プレスリリース. 2024-01-04. ; Gene expression technology set to semi-automation: KyotoU develops RENGE to infer gene regulatory networks efficiently and accurately. 京都大学プレスリリース. 2024-03-14. ; Single-cell RNA-seq analysis coupled with CRISPR-based perturbation has enabled the inference of gene regulatory networks with causal relationships. However, a snapshot of single-cell CRISPR data may not lead to an accurate inference, since a gene knockout can influence multi-layered downstream over time. Here, we developed RENGE, a computational method that infers gene regulatory networks using a time-series single-cell CRISPR dataset. RENGE models the propagation process of the effects elicited by a gene knockout on its regulatory network. It can distinguish between direct and indirect regulations, which allows for the inference of regulations by genes that are not knocked out. RENGE therefore outperforms current methods in the accuracy of inferring gene regulatory networks. When used on a dataset we derived from human-induced pluripotent stem cells, RENGE yielded a network consistent with multiple databases and literature. Accurate inference of gene regulatory networks by RENGE would enable the identification of key factors for various biological systems. |
| نوع الوثيقة: |
article in journal/newspaper |
| اللغة: |
English |
| تدمد: |
2399-3642 |
| Relation: |
https://www.kyoto-u.ac.jp/ja/research-news/2024-01-04; https://www.kyoto-u.ac.jp/en/research-news/2024-03-14; http://hdl.handle.net/2433/286528; Communications Biology; 1290 |
| الاتاحة: |
http://hdl.handle.net/2433/286528 |
| Rights: |
© The Author(s) 2023 ; This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. ; http://creativecommons.org/licenses/by/4.0/ |
| رقم الانضمام: |
edsbas.A93513F3 |
| قاعدة البيانات: |
BASE |
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