JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.
复制标题
DOI：
10.1093/nar/gkx1188
复制
发表时间：
2018-01-04
影响因子：
14.9
通讯作者：
Mathelier A
中科院分区：
文献类型：
--
作者：
Khan A;Fornes O;Stigliani A;Gheorghe M;Castro-Mondragon JA;van der Lee R;Bessy A;Chèneby J;Kulkarni SR;Tan G;Baranasic D;Arenillas DJ;Sandelin A;Vandepoele K;Lenhard B;Ballester B;Wasserman WW;Parcy F;Mathelier A
JASPAR（http：jaspar.genereg.net）是一个开放访问的数据库，其中包含以位置频率矩阵（PFM）和TF灵活模型（TFFM）形式存储的6个分类组中多个物种的TF的精选、非冗余转录因子（TF）结合谱。在2018年发布的JASPAR中，CORE收集了322个新的PFMs（60个用于脊椎动物，262个用于植物），并更新了33个PFMs（24个用于脊椎动物，8个用于植物，1个用于昆虫）。与2016年版本相比，这些新配置文件扩展了30%。此外，我们还引进了316个TFFMs（95个脊椎动物，218个植物和3个昆虫）。该版本在每个分类单元和每个分类单元的每个TF类别中包含了相似的PFMs集群。JASPAR 2018 CORE脊椎动物PFMs集合用于预测人类基因组中的TF结合位点。这些预测通过UCSC基因组浏览器跟踪数据中心提供给科学界。最后，这次更新带来了一个新的Web框架，具有交互式和响应式用户界面，沿着新功能。所有底层数据都可以使用RESTful API和JASPAR 2018 R/Bioconductor包以编程方式检索。
JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six taxonomic groups. In the 2018 release of JASPAR, the CORE collection has been expanded with 322 new PFMs (60 for vertebrates and 262 for plants) and 33 PFMs were updated (24 for vertebrates, 8 for plants and 1 for insects). These new profiles represent a 30% expansion compared to the 2016 release. In addition, we have introduced 316 TFFMs (95 for vertebrates, 218 for plants and 3 for insects). This release incorporates clusters of similar PFMs in each taxon and each TF class per taxon. The JASPAR 2018 CORE vertebrate collection of PFMs was used to predict TF-binding sites in the human genome. The predictions are made available to the scientific community through a UCSC Genome Browser track data hub. Finally, this update comes with a new web framework with an interactive and responsive user-interface, along with new features. All the underlying data can be retrieved programmatically using a RESTful API and through the JASPAR 2018 R/Bioconductor package.
影响因子：
14.9
作者：
Khan A;Fornes O;Stigliani A;Gheorghe M;Castro-Mondragon JA;van der Lee R;Bessy A;Chèneby J;Kulkarni SR;Tan G;Baranasic D;Arenillas DJ;Sandelin A;Vandepoele K;Lenhard B;Ballester B;Wasserman WW;Parcy F;Mathelier A
通讯作者：
Mathelier A