Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
Nat Protoc. 2010 Feb;5(2):303-22. doi: 10.1038/nprot.2009.230. Epub 2010 Jan 28.
A major challenge in the analysis of gene expression microarray data is to extract meaningful biological knowledge out of the huge volume of raw data. Expander (EXPression ANalyzer and DisplayER) is an integrated software platform for the analysis of gene expression data, which is freely available for academic use. It is designed to support all the stages of microarray data analysis, from raw data normalization to inference of transcriptional regulatory networks. The microarray analysis described in this protocol starts with importing the data into Expander 5.0 and is followed by normalization and filtering. Then, clustering and network-based analyses are performed. The gene groups identified are tested for enrichment in function (based on Gene Ontology), co-regulation (using transcription factor and microRNA target predictions) or co-location. The results of each analysis step can be visualized in a number of ways. The complete protocol can be executed in approximately 1 h.
基因表达微阵列数据分析的主要挑战是从大量原始数据中提取有意义的生物学知识。Expander（EXPression ANalyzer 和 DisplayER）是一个用于基因表达数据分析的集成软件平台，可免费供学术使用。它旨在支持微阵列数据分析的所有阶段，从原始数据标准化到转录调控网络的推断。本协议中描述的微阵列分析从将数据导入 Expander 5.0 开始，然后进行标准化和过滤。然后，进行聚类和基于网络的分析。识别的基因组将基于功能（基于基因本体论）、共调控（使用转录因子和 microRNA 靶标预测）或共定位进行富集测试。可以以多种方式可视化每个分析步骤的结果。整个协议大约需要 1 小时才能完成。
