Dipartimento di Scienze Biomolecolari e Biotecnologie, Università di Milano, Italy.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W510-5. doi: 10.1093/nar/gks483. Epub 2012 Jun 4.
The regulation of transcription of eukaryotic genes is a very complex process, which involves interactions between transcription factors (TFs) and DNA, as well as other epigenetic factors like histone modifications, DNA methylation, and so on, which nowadays can be studied and characterized with techniques like ChIP-Seq. Cscan is a web resource that includes a large collection of genome-wide ChIP-Seq experiments performed on TFs, histone modifications, RNA polymerases and others. Enriched peak regions from the ChIP-Seq experiments are crossed with the genomic coordinates of a set of input genes, to identify which of the experiments present a statistically significant number of peaks within the input genes' loci. The input can be a cluster of co-expressed genes, or any other set of genes sharing a common regulatory profile. Users can thus single out which TFs are likely to be common regulators of the genes, and their respective correlations. Also, by examining results on promoter activation, transcription, histone modifications, polymerase binding and so on, users can investigate the effect of the TFs (activation or repression of transcription) as well as of the cell or tissue specificity of the genes' regulation and expression. The web interface is free for use, and there is no login requirement. Available at: http://www.beaconlab.it/cscan.
真核基因转录的调控是一个非常复杂的过程，涉及转录因子（TFs）与 DNA 之间的相互作用，以及其他表观遗传因子，如组蛋白修饰、DNA 甲基化等，这些因子现在可以通过 ChIP-Seq 等技术进行研究和表征。Cscan 是一个网络资源，其中包含大量在 TFs、组蛋白修饰、RNA 聚合酶等上进行的全基因组 ChIP-Seq 实验。ChIP-Seq 实验中的富集峰区域与一组输入基因的基因组坐标交叉，以确定输入基因座内有多少个实验呈现出统计学上显著的峰。输入可以是一组共表达基因，也可以是任何其他具有共同调控特征的基因集。用户因此可以确定哪些 TF 可能是基因的常见调控因子，以及它们各自的相关性。此外，通过检查启动子激活、转录、组蛋白修饰、聚合酶结合等方面的结果，用户可以研究 TF 的作用（转录的激活或抑制）以及基因调控和表达的细胞或组织特异性。该网络界面可供免费使用，无需登录。网址：http://www.beaconlab.it/cscan。
