HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis.
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis.
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DOI：
10.1093/nar/gkx1106
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发表时间：
2018-01-04
影响因子：
14.9
通讯作者：
Makeev VJ
中科院分区：
文献类型：
--
作者：
Kulakovskiy IV;Vorontsov IE;Yevshin IS;Sharipov RN;Fedorova AD;Rumynskiy EI;Medvedeva YA;Magana-Mora A;Bajic VB;Papatsenko DA;Kolpakov FA;Makeev VJ
我们提出了一个重大更新的HOCOMOCO收集，包括模式描述DNA结合特异性的人类和小鼠转录因子。在这个版本中，我们受益于近两倍的已发表的转录因子（TF）结合的体内实验，以扩大结合模型的库，取代以前仅基于体外数据的低质量模型，并覆盖了100多个具有以前未知的结合特异性的TF。这是通过在BioUML框架内使用几种ChIP-Seq峰调用工具统一处理并在GTRD数据库中聚合的5000多个ChIP-Seq实验的系统基序发现来实现的。HOCOMOCO v11包含453个小鼠和680个人类转录因子的结合模型，包括1302个单核苷酸和576个二核苷酸位置权重矩阵，描述了每个转录因子的主要结合偏好和可靠的替代结合特异性。互动界面和批量下载可在网站上获得：http://hocomoco.autosome.ru和http://www.cbrc.kaust.edu.sa/hocomoco11。在此版本中，我们通过MoLoTool（Motif Location）补充了HOCOMOCO，该工具应用HOCOMOCO模型来可视化短DNA序列中的结合位点。http://molotool.autosome.ru
We present a major update of the HOCOMOCO collection that consists of patterns describing DNA binding specificities for human and mouse transcription factors. In this release, we profited from a nearly doubled volume of published in vivo experiments on transcription factor (TF) binding to expand the repertoire of binding models, replace low-quality models previously based on in vitro data only and cover more than a hundred TFs with previously unknown binding specificities. This was achieved by systematic motif discovery from more than five thousand ChIP-Seq experiments uniformly processed within the BioUML framework with several ChIP-Seq peak calling tools and aggregated in the GTRD database. HOCOMOCO v11 contains binding models for 453 mouse and 680 human transcription factors and includes 1302 mononucleotide and 576 dinucleotide position weight matrices, which describe primary binding preferences of each transcription factor and reliable alternative binding specificities. An interactive interface and bulk downloads are available on the web: http://hocomoco.autosome.ru and http://www.cbrc.kaust.edu.sa/hocomoco11. In this release, we complement HOCOMOCO by MoLoTool (Motif Location Toolbox, http://molotool.autosome.ru) that applies HOCOMOCO models for visualization of binding sites in short DNA sequences.
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影响因子：
14.9
作者：
Maaskola J;Rajewsky N
通讯作者：
Rajewsky N
影响因子：
4.4
作者：
Levitsky VG;Kulakovskiy IV;Ershov NI;Oshchepkov DY;Makeev VJ;Hodgman TC;Merkulova TI
通讯作者：
Merkulova TI
影响因子：
4.3
作者：
Guo Y;Mahony S;Gifford DK
通讯作者：
Gifford DK
影响因子：
3.7
作者：
Boeva V
通讯作者：
Boeva V
影响因子：
14.9
作者：
Bailey TL;Johnson J;Grant CE;Noble WS
通讯作者：
Noble WS