Di Cara Alessandro, Schmidt Karsten, Hemmings Brian A, Oakeley Edward J
Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W423-6. doi: 10.1093/nar/gki413.
PromoterPlot (http://promoterplot.fmi.ch) is a web-based tool for simplifying the display and processing of transcription factor searches using either the commercial or free TransFac distributions. The input sequence is a TransFac search (public version) or FASTA/Affymetrix IDs (local install). It uses an intuitive pattern recognition algorithm for finding similarities between groups of promoters by dividing transcription factor predictions into conserved triplet models. To minimize the number of false-positive models, it can optionally exclude factors that are known to be unexpressed or inactive in the cells being studied based on microarray or proteomic expression data. The program will also estimate the likelihood of finding a pattern by chance based on the frequency observed in a control set of mammalian promoters we obtained from Genomatix. The results are stored as an interactive SVG web page on our server.
启动子图谱工具（http://promoterplot.fmi.ch）是一个基于网络的工具，用于简化使用商业版或免费版TransFac数据库进行转录因子搜索的显示和处理。输入序列可以是TransFac搜索（公共版本）或FASTA/Affymetrix ID（本地安装）。它使用直观的模式识别算法，通过将转录因子预测分为保守三联体模型来寻找启动子组之间的相似性。为了尽量减少假阳性模型的数量，它可以根据微阵列或蛋白质组表达数据，选择性地排除已知在被研究细胞中未表达或无活性的因子。该程序还将根据我们从Genomatix获得的一组哺乳动物启动子对照集中观察到的频率，估计偶然发现一种模式的可能性。结果作为交互式SVG网页存储在我们的服务器上。
