Array2BIO: from microarray expression data to functional annotation of co-regulated genesReportar como inadecuado




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BMC Bioinformatics

, 7:307

First Online: 16 June 2006Received: 21 March 2006Accepted: 16 June 2006

Abstract

BackgroundThere 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.

ResultsArray2BIO 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.

ConclusionWe 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.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-7-307 contains supplementary material, which is available to authorized users.

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Autor: Gabriela G Loots - Patrick SG Chain - Shalini Mabery - Amy Rasley - Emilio Garcia - Ivan Ovcharenko

Fuente: https://link.springer.com/



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