JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles.
JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles.
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DOI：
10.1093/nar/gkv1176
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发表时间：
2016-01-04
影响因子：
14.9
通讯作者：
Wasserman WW
中科院分区：
文献类型：
--
作者：
Mathelier A;Fornes O;Arenillas DJ;Chen CY;Denay G;Lee J;Shi W;Shyr C;Tan G;Worsley-Hunt R;Zhang AW;Parcy F;Lenhard B;Sandelin A;Wasserman WW
Jaspar（http://jaspar.genereg.net）是一种开放式数据库，该数据库存储策划的，非冗余的转录因子（TF）结合曲线，代表转录因子结合偏好为六个分类组中多种物种的位置频率矩阵。在2016年发行版中，我们使用494个新的TF结合轮廓扩展了Jaspar Core Collection（脊椎动物315个，在昆虫中115个，昆虫中有11个，真菌164个，植物中的164个），并更新了59个配置文件（脊椎动物58个，脊椎动物中的1个。 ）。与先前的版本相比，引入的配置文件代表83％的扩展和10％的更新。我们更新了发布的分层结构分类后，更新了TF DNA结合域（DBD）的结构注释。此外，我们引入了130个转录因子柔性模型，该模型在脊椎动物的CHIP-SEQ数据上训练，这些模型捕获了TF结合位点内的二核苷酸依赖性。这个新的Jaspar发行版伴随着一种新的Web工具来推断以给定TF蛋白序列识别的Jaspar TF结合轮廓。此外，我们为用户提供了一个Ruby模块，以补充Jaspar API，以简化jaspar配置文件集合的程序化访问和使用。最后，我们提供JASPAR2016 R/Bioconductor数据包以及此版本的数据。
JASPAR (http://jaspar.genereg.net) is an open-access database storing curated, non-redundant transcription factor (TF) binding profiles representing transcription factor binding preferences as position frequency matrices for multiple species in six taxonomic groups. For this 2016 release, we expanded the JASPAR CORE collection with 494 new TF binding profiles (315 in vertebrates, 11 in nematodes, 3 in insects, 1 in fungi and 164 in plants) and updated 59 profiles (58 in vertebrates and 1 in fungi). The introduced profiles represent an 83% expansion and 10% update when compared to the previous release. We updated the structural annotation of the TF DNA binding domains (DBDs) following a published hierarchical structural classification. In addition, we introduced 130 transcription factor flexible models trained on ChIP-seq data for vertebrates, which capture dinucleotide dependencies within TF binding sites. This new JASPAR release is accompanied by a new web tool to infer JASPAR TF binding profiles recognized by a given TF protein sequence. Moreover, we provide the users with a Ruby module complementing the JASPAR API to ease programmatic access and use of the JASPAR collection of profiles. Finally, we provide the JASPAR2016 R/Bioconductor data package with the data of this release.