RTFBSDB: an integrated framework for transcription factor binding site analysis.
RTFBSDB: an integrated framework for transcription factor binding site analysis.
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RTFBSDB：转录因子结合位点分析的集成框架。
DOI：
10.1093/bioinformatics/btw338
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发表时间：
2016
期刊：
影响因子：
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通讯作者：
Danko,CharlesG
中科院分区：
文献类型：
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作者：
Wang,Zhong;Martins,AndréL;Danko,CharlesG
转录因子通过与短的DNA序列基序结合来调节基因转录的复杂程序。在这里，我们介绍rtfbsdb，一个统一的框架，集成了超过65 000 TF结合基序的数据库与工具，轻松，高效地扫描目标基因组序列。Rtfbsdb将具有相似DNA序列特异性的基序聚类，并整合RNA-seq或PRO-seq数据，以将分析限制在由感兴趣的细胞类型中表达的TF识别的基序。我们的软件包允许在集成环境中快速执行常见分析。可用性和实施：rtfbsdb可在（https：//github.com/Danko-Lab/rtfbs_db）获得。联系方式：dankoc@gmail. com补充信息：补充数据可在Bioinformatics online获得。
Summary:Transcription factors (TFs) regulate complex programs of gene transcription by binding to short DNA sequence motifs. Here, we introduce rtfbsdb, a unified framework that integrates a database of more than 65 000 TF binding motifs with tools to easily and efficiently scan target genome sequences. Rtfbsdb clusters motifs with similar DNA sequence specificities and integrates RNA-seq or PRO-seq data to restrict analyses to motifs recognized by TFs expressed in the cell type of interest. Our package allows common analyses to be performed rapidly in an integrated environment.Availability and Implementation:rtfbsdbavailable at (https://github.com/Danko-Lab/rtfbs_db).Contact:dankoc@gmail.comSupplementary information:Supplementary data are available atBioinformaticsonline.