School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA.
Bioinformatics. 2010 Jan 15;26(2):168-74. doi: 10.1093/bioinformatics/btp657. Epub 2009 Dec 2.
There is accumulating evidence that the chromatin environment of transcription factor (TF) binding sites in promoter regions has a critical influence on their regulatory potential. Recent studies have mapped TF binding sites and nucleosome positions throughout the yeast genome; however, there is a lack of computation tools to integrate these data types.
We have developed the Ceres software to facilitate the integrated analysis of TF binding sites and nucleosome positions in the model eukaryote S. cerevisiae. Ceres enables users to dynamically display the spatial organization of TF binding sites and nucleosome positions of individual genes, or the average profiles for large gene sets. Ceres provides novel statistical tools to test for the enrichment of TF binding sites and chromatin environments for user-selected gene sets. Ceres also enables users to search the genome for combinations of TF binding sites that are associated with specific chromatin environments. Preliminary analysis using the Ceres software indicates that functional and conserved TF binding sites are often associated with specific chromatin environments.
http://bioinformatics1.smb.wsu.edu/Ceres.
Supplementary data are available at Bioinformatics online.
越来越多的证据表明，转录因子（TF）结合位点在启动子区域的染色质环境对其调控潜力具有关键影响。最近的研究已经绘制了整个酵母基因组中 TF 结合位点和核小体位置的图谱；然而，缺乏计算工具来整合这些数据类型。
我们开发了 Ceres 软件，以方便对模型真核生物 S. cerevisiae 中的 TF 结合位点和核小体位置进行综合分析。Ceres 使用户能够动态显示单个基因的 TF 结合位点和核小体位置的空间组织，或大量基因集的平均图谱。Ceres 为用户选择的基因集提供了新颖的统计工具，用于测试 TF 结合位点和染色质环境的富集。Ceres 还使用户能够在基因组中搜索与特定染色质环境相关的 TF 结合位点组合。使用 Ceres 软件进行的初步分析表明，功能和保守的 TF 结合位点通常与特定的染色质环境相关。
http://bioinformatics1.smb.wsu.edu/Ceres。
补充数据可在 Bioinformatics 在线获得。
