CressInt: a user-friendly web resource for genome-scale exploration of gene regulation in Arabidopsis thaliana.
CressInt: a user-friendly web resource for genome-scale exploration of gene regulation in Arabidopsis thaliana.
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DOI：
10.1016/j.cpb.2015.09.001
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发表时间：
2015-09
影响因子：
5.4
通讯作者：
Weirauch MT
中科院分区：
文献类型：
--
作者：
Chen X;Ernst K;Soman F;Borowczak M;Weirauch MT
拟南芥（Arabidopsis thaliana）是研究多种生物过程的强大模式生物。最近测序技术的进步已经产生了丰富的信息，描述了拟南芥基因组功能的许多方面。然而，相对缺乏有效地使用这些数据来创建可测试假设的计算系统。我们提出了cresint，一个用户友好的网络资源，用于在基因组规模上探索拟南芥的基因调控机制。CressInt系统整合了多种与基因调控相关的全基因组数据类型，包括转录因子（TF）结合位点模型、ChIP-seq、dna -seq、eQTLs和GWAS。我们通过展示如何使用该系统来证明CressInt的实用性：(1)识别与感兴趣的基因启动子结合的tf；(2)基于ChIP-seq数据集识别可能影响TF结合的遗传变异；(3)鉴定其结合可能受到表型相关变异影响的特异性tf。CressInt可以在http://cressint.cchmc.org免费获得。
The thale cress Arabidopsis thaliana is a powerful model organism for studying a wide variety of biological processes. Recent advances in sequencing technology have resulted in a wealth of information describing numerous aspects of A. thaliana genome function. However, there is a relative paucity of computational systems for efficiently and effectively using these data to create testable hypotheses. We present CressInt, a user-friendly web resource for exploring gene regulatory mechanisms in A. thaliana on a genomic scale. The CressInt system incorporates a variety of genome-wide data types relevant to gene regulation, including transcription factor (TF) binding site models, ChIP-seq, DNase-seq, eQTLs, and GWAS. We demonstrate the utility of CressInt by showing how the system can be used to (1) Identify TFs binding to the promoter of a gene of interest; (2) identify genetic variants that are likely to impact TF binding based on a ChIP-seq dataset; and (3) identify specific TFs whose binding might be impacted by phenotype-associated variants. CressInt is freely available at http://cressint.cchmc.org.