Update of the FANTOM web resource: enhancement for studying noncoding genomes

IF 16.6 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Nucleic Acids Research Pub Date : 2024-11-27 DOI:10.1093/nar/gkae1047

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

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Abstract

The FANTOM web resource (https://fantom.gsc.riken.jp/) has been a unique resource for studying mammalian genomes, which is built on the research activities conducted in the international collaborative project FANTOM (Functional ANnoTation Of the Mammalian genome). In recent updates, we expanded annotations for long non-coding RNAs (lncRNAs) and transcribed cis-regulatory elements (CREs). The former was derived from the large-scale lncRNA perturbations in induced pluripotent stem cells (iPSCs) and integrative analysis of Hi-C data conducted in the sixth iteration of the project (FANTOM6). The resulting annotations of lncRNAs, according to the impact on cellular and molecular phenotypes and the potential RNA-chromatin interactions, are accessible via the interactive ZENBU-Reports framework. The latter involves a new platform, fanta.bio (https://fanta.bio/), which collects transcribed CREs identified via use of an extended dataset of CAGE profiles. The CREs, with their annotations including genetic and epigenetic information, are accessible via a dedicated interface as well as the UCSC Genome Browser Database. These updates offer enhanced opportunities to investigate the functions of non-coding regions within mammalian genomes.

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FANTOM 网络资源（https://fantom.gsc.riken.jp/）是研究哺乳动物基因组的独特资源，它建立在国际合作项目 FANTOM（哺乳动物基因组功能注释）的研究活动基础之上。在最近的更新中，我们扩展了长非编码 RNA（lncRNA）和转录顺式调控元件（CRE）的注释。前者来自诱导多能干细胞（iPSCs）中的大规模 lncRNA 干扰以及项目第六次迭代（FANTOM6）中对 Hi-C 数据的综合分析。根据对细胞和分子表型的影响以及潜在的RNA-染色质相互作用对lncRNA进行的注释可通过交互式ZENBU-Reports框架访问。后者涉及一个新平台，fanta.bio (https://fanta.bio/)，该平台收集通过使用 CAGE 配置文件的扩展数据集确定的转录 CREs。CREs 及其注释（包括遗传和表观遗传信息）可通过专用界面和 UCSC 基因组浏览器数据库访问。这些更新为研究哺乳动物基因组中非编码区的功能提供了更多机会。

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来源期刊

Nucleic Acids Research 生物-生化与分子生物学

CiteScore

27.10

自引率

4.70%

发文量

1057

审稿时长

2 months

期刊介绍： Nucleic Acids Research (NAR) is a scientific journal that publishes research on various aspects of nucleic acids and proteins involved in nucleic acid metabolism and interactions. It covers areas such as chemistry and synthetic biology, computational biology, gene regulation, chromatin and epigenetics, genome integrity, repair and replication, genomics, molecular biology, nucleic acid enzymes, RNA, and structural biology. The journal also includes a Survey and Summary section for brief reviews. Additionally, each year, the first issue is dedicated to biological databases, and an issue in July focuses on web-based software resources for the biological community. Nucleic Acids Research is indexed by several services including Abstracts on Hygiene and Communicable Diseases, Animal Breeding Abstracts, Agricultural Engineering Abstracts, Agbiotech News and Information, BIOSIS Previews, CAB Abstracts, and EMBASE.