Software

Array2BIO: from microarray expression data to functional annotation of co-regulated genes

Gabriela G Loots¹ , Patrick SG Chain^1,3 , Shalini Mabery¹ , Amy Rasley¹ , Emilio Garcia¹ and Ivan Ovcharenko^1,2

¹Biosciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA

²Computational Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA

³Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA

author email corresponding author email

BMC Bioinformatics 2006, 7:307doi:10.1186/1471-2105-7-307

Published:	16 June 2006

Abstract

Background

There are several isolated tools for partial analysis of microarray expression data. To provide an integrative, easy-to-use and automated toolkit for the analysis of Affymetrix microarray expression data we have developed Array2BIO, an application that couples several analytical methods into a single web based utility.

Results

Array2BIO converts raw intensities into probe expression values, automatically maps those to genes, and subsequently identifies groups of co-expressed genes using two complementary approaches: (1) comparative analysis of signal versus control and (2) clustering analysis of gene expression across different conditions. The identified genes are assigned to functional categories based on Gene Ontology classification and KEGG protein interaction pathways. Array2BIO reliably handles low-expressor genes and provides a set of statistical methods for quantifying expression levels, including Benjamini-Hochberg and Bonferroni multiple testing corrections. An automated interface with the ECR Browser provides evolutionary conservation analysis for the identified gene loci while the interconnection with Crème allows prediction of gene regulatory elements that underlie observed expression patterns.

Conclusion

We have developed Array2BIO – a web based tool for rapid comprehensive analysis of Affymetrix microarray expression data, which also allows users to link expression data to Dcode.org comparative genomics tools and integrates a system for translating co-expression data into mechanisms of gene co-regulation. Array2BIO is publicly available at http://array2bio.dcode.org. webcite