Bioinformatic Tools for Inferring Functional Information from Plant Microarray Data II: Analysis Beyond Single Gene

Issa Coulibaly,Grier P Page

doi:10.1155/2008/893941

Issa Coulibaly, Grier P Page

Open Access

https://doi.org/10.1155/2008/893941

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Abstract

While it is possible to interpret microarray experiments a single gene at a time, most studies generate long lists of differentially expressed genes whose interpretation requires the integration of prior biological knowledge. This prior knowledge is stored in various public and private databases and covers several aspects of gene function and biological information. In this review, we will describe the tools and places where to find prior accurate biological information and how to process and incorporate them to interpret microarray data analyses. Here, we highlight selected tools and resources for gene class level ontology analysis (Section 2), gene coexpression analysis (Section 3), gene network analysis (Section 4), biological pathway analysis (Section 5), analysis of transcriptional regulation (Section 6), and omics data integration (Section 7). The overall goal of this review is to provide researchers with tools and information to facilitate the interpretation of microarray data.

Highlights

Microarray analysis is exploratory and very high dimensional, and the primary purpose is to generate a list of differentially regulated genes that can provide insight into the biological phenomena under investigation
Combining microarray data with prior biological knowledge is a fundamental key to the interpretation of the list of genes
We address some theoretical aspects and methodological issues of the algorithms implemented in the tools that have been recently developed for bioinformatic and what needs to be considered when selecting a tool for use

Summary

Introduction

Microarray analysis is exploratory and very high dimensional, and the primary purpose is to generate a list of differentially regulated genes that can provide insight into the biological phenomena under investigation. Combining microarray data with prior biological knowledge is a fundamental key to the interpretation of the list of genes. This prior knowledge is stored in various public and private databases and covers several aspects of genes functions and biological information such as regulatory sequence analysis, gene ontology, and pathway information. We will describe the tools and places where to find prior accurate biological information and how to incorporate them into the analysis of microarray data.

Objectives

Methods

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Conclusion