JASPAR 2022:转录因子结合谱开放获取数据库的第 9 个版本。

JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles.

机构信息

Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway.

Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrsF-38054, Grenoble, France.

出版信息

Nucleic Acids Res. 2022 Jan 7;50(D1):D165-D173. doi: 10.1093/nar/gkab1113.

Abstract

JASPAR (http://jaspar.genereg.net/) is an open-access database containing manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six taxonomic groups. In this 9th release, we expanded the CORE collection with 341 new profiles (148 for plants, 101 for vertebrates, 85 for urochordates, and 7 for insects), which corresponds to a 19% expansion over the previous release. We added 298 new profiles to the Unvalidated collection when no orthogonal evidence was found in the literature. All the profiles were clustered to provide familial binding profiles for each taxonomic group. Moreover, we revised the structural classification of DNA binding domains to consider plant-specific TFs. This release introduces word clouds to represent the scientific knowledge associated with each TF. We updated the genome tracks of TFBSs predicted with JASPAR profiles in eight organisms; the human and mouse TFBS predictions can be visualized as native tracks in the UCSC Genome Browser. Finally, we provide a new tool to perform JASPAR TFBS enrichment analysis in user-provided genomic regions. All the data is accessible through the JASPAR website, its associated RESTful API, the R/Bioconductor data package, and a new Python package, pyJASPAR, that facilitates serverless access to the data.

摘要

JASPAR(http://jaspar.genereg.net/)是一个开放获取的数据库,其中包含跨六个分类群的转录因子(TF)的手动整理、非冗余的转录因子结合谱。在这个第 9 个版本中,我们扩展了 CORE 集合,增加了 341 个新的图谱(植物 148 个,脊椎动物 101 个,尾索动物 85 个,昆虫 7 个),与上一个版本相比增加了 19%。当在文献中没有发现正交证据时,我们在未验证集合中添加了 298 个新图谱。所有图谱都进行了聚类,为每个分类群提供了家族结合图谱。此外,我们修订了 DNA 结合域的结构分类,以考虑植物特异性 TF。此版本引入了词云,以表示与每个 TF 相关的科学知识。我们更新了在八个生物体中使用 JASPAR 图谱预测的 TFBS 基因组图谱;人类和小鼠 TFBS 预测可以在 UCSC 基因组浏览器中作为本地轨道可视化。最后,我们提供了一个新工具,用于在用户提供的基因组区域中执行 JASPAR TFBS 富集分析。所有数据都可以通过 JASPAR 网站、其相关的 RESTful API、R/Bioconductor 数据包以及新的 Python 包 pyJASPAR 访问,后者方便了对数据的无服务器访问。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9566/8728201/621103e87b67/gkab1113fig1.jpg

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