IARRAY - Vol 22 no 13 2006 pages 1665–1667...

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Unformatted text preview: Vol. 22 no. 13 2006, pages 1665–1667 doi:10.1093/bioinformatics/btl163 BIOINFORMATICS APPLICATIONS NOTE Gene expression Integrative Array Analyzer: a software package for analysis of cross-platform and cross-species microarray data Fei Pan 1,† , Kiran Kamath 1,† , Kangyu Zhang 1 , Sudip Pulapura 1 , Avinash Achar 1 , Juan Nunez-Iglesias 1 , Yu Huang 1 , Xifeng Yan 2 , Jiawei Han 2 , Haiyan Hu 1 , Min Xu 1 , Jianjun Hu 1 and Xianghong Jasmine Zhou 1, Ã 1 Program in Molecular and Computational Biology, University of Southern California, Los Angeles, USA and 2 Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Received on February 16, 2006; revised on March 23, 2006; accepted on April 24, 2006 Advance Access publication May 3, 2006 Associate Editor: Joaquin Dopazo ABSTRACT Summary: The rapid accumulation of microarray data translates into an urgent need for tools to perform integrative microarray analysis. Integrative Array Analyzer is a comprehensive analysis and visualiza- tion software toolkit, which aims to facilitate the reuse of the large amount of cross-platform and cross-species microarray data. It is composed of the data preprocess module, the co-expression analysis module, the differential expression analysis module, the functional and transcriptional annotation module and the graph visualization module. Availability: http://zhoulab.usc.edu Contact: [email protected] 1 INTRODUCTION Microarray gene expression profiling has been conducted in many laboratories, resulting in a rapid accumulation of data in public repositories. Although there are many advantages to combine microarray datasets for integrative analysis, it is not a trivial task to integrate cross-platform microarray datasets. The existence of different microarray technology and alternative experimental para- meters (e.g. use of direct or indirect labeling, choice of controls, choice of different scanner and image analysis software) results in systematic variations among datasets that are often beyond the capability of statistical normalization. Recently, several studies have begun to address these issues and have proposed statistical and computational methods to assess expression patterns concord- ant among several microarray datasets (Choi et al ., 2003; Hu et al ., 2005; Lamb et al ., 2003; Lee et al ., 2004; Rhodes et al ., 2002; Segal et al ., 2004; Zhou et al ., 2005). Yet, there lack software tools for biologists to perform integrative analysis of multiple microarray datasets. Here, we report the first comprehensive analysis software toolkit, Integrative Array Analyzer (‘ iArray ’ in short), for platform- independent integration of microarray datasets....
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IARRAY - Vol 22 no 13 2006 pages 1665–1667...

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