Zhang Yan, Luoh Shiuh-Ming, Hon Lawrence S, Baertsch Robert, Wood William I, Zhang Zemin
Department of Bioinformatics, Genentech, Inc., South San Francisco, CA 94080, USA.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W152-8. doi: 10.1093/nar/gkm381. Epub 2007 Jun 1.
GeneHub-GEPIS is a web application that performs digital expression analysis in human and mouse tissues based on an integrated gene database. Using aggregated expressed sequence tag (EST) library information and EST counts, the application calculates the normalized gene expression levels across a large panel of normal and tumor tissues, thus providing rapid expression profiling for a given gene. The backend GeneHub component of the application contains pre-defined gene structures derived from mRNA transcript sequences from major databases and includes extensive cross references for commonly used gene identifiers. ESTs are then linked to genes based on their precise genomic locations as determined by GMAP. This genome-based approach reduces incorrect matches between ESTs and genes, thus minimizing the noise seen with previous tools. In addition, the gene-centric design makes it possible to add several important features, including text searching capabilities, the ability to accept diverse input values, expression analysis for microRNAs, basic gene annotation, batch analysis and linking between mouse and human genes. GeneHub-GEPIS is available at http://www.cgl.ucsf.edu/Research/genentech/genehub-gepis/ or http://www.gepis.org/.
GeneHub - GEPIS是一个基于整合基因数据库在人类和小鼠组织中进行数字表达分析的网络应用程序。该应用程序利用聚合表达序列标签（EST）文库信息和EST计数，计算大量正常和肿瘤组织中的标准化基因表达水平，从而为给定基因提供快速表达谱分析。该应用程序的后端GeneHub组件包含从主要数据库的mRNA转录序列派生的预定义基因结构，并包括常用基因标识符的广泛交叉引用。然后，根据GMAP确定的精确基因组位置将EST与基因链接起来。这种基于基因组的方法减少了EST与基因之间的错误匹配，从而将先前工具中出现的噪声降至最低。此外，以基因为中心的设计使得添加几个重要功能成为可能，包括文本搜索功能、接受不同输入值的能力、微小RNA的表达分析、基本基因注释、批量分析以及小鼠和人类基因之间的链接。可通过http://www.cgl.ucsf.edu/Research/genentech/genehub - gepis/ 或http://www.gepis.org/访问GeneHub - GEPIS。
