Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, 20133 Milano, Italy.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W535-43. doi: 10.1093/nar/gkt448. Epub 2013 Jun 7.
Chromatin immunoprecipitation followed by sequencing with next-generation technologies (ChIP-Seq) has become the de facto standard for building genome-wide maps of regions bound by a given transcription factor (TF). The regions identified, however, have to be further analyzed to determine the actual DNA-binding sites for the TF, as well as sites for other TFs belonging to the same TF complex or in general co-operating or interacting with it in transcription regulation. PscanChIP is a web server that, starting from a collection of genomic regions derived from a ChIP-Seq experiment, scans them using motif descriptors like JASPAR or TRANSFAC position-specific frequency matrices, or descriptors uploaded by users, and it evaluates both motif enrichment and positional bias within the regions according to different measures and criteria. PscanChIP can successfully identify not only the actual binding sites for the TF investigated by a ChIP-Seq experiment but also secondary motifs corresponding to other TFs that tend to bind the same regions, and, if present, precise positional correlations among their respective sites. The web interface is free for use, and there is no login requirement. It is available at http://www.beaconlab.it/pscan_chip_dev.
染色质免疫沉淀结合新一代测序技术（ChIP-Seq）已成为构建特定转录因子（TF）结合基因组区域图谱的事实上的标准。然而，所鉴定的区域必须进一步进行分析，以确定 TF 的实际 DNA 结合位点，以及属于同一 TF 复合物或一般在转录调控中与其合作或相互作用的其他 TF 的结合位点。PscanChIP 是一个 Web 服务器，它从 ChIP-Seq 实验中获得的一组基因组区域开始，使用 JASPAR 或 TRANSFAC 位置特异性频率矩阵等 motif 描述符，或用户上传的描述符对它们进行扫描，并根据不同的测量和标准评估区域内的 motif 富集和位置偏向。PscanChIP 不仅可以成功识别 ChIP-Seq 实验中研究的 TF 的实际结合位点，还可以识别对应于其他倾向于结合相同区域的 TF 的二级 motif，如果存在的话，还可以识别它们各自位点之间的精确位置相关性。该 Web 界面可免费使用，无需登录。它可在 http://www.beaconlab.it/pscan_chip_dev 上获得。
