Bioinformatic Tools for Inferring Functional Information from Plant Microarray Data: Tools for the First Steps

Microarrays are a very powerful tool for quantifying the amount of RNA in samples; however, their ability to query essentially every gene in a genome, which can number in the tens of thousands, presents analytical and interpretative problems. As a result, a variety of software and web-based tools have been developed to help with these issues. This article highlights and reviews some of the tools for the first steps in the analysis of a microarray study. We have tried for a balance between free and commercial systems. We have organized the tools by topics including image processing tools ( Section 2 ), power analysis tools ( Section 3 ), image analysis tools ( Section 4 ), database tools ( Section 5 ), databases of functional information ( Section 6 ), annotation tools ( Section 7 ), statistical and data mining tools ( Section 8 ), and dissemination tools ( Section 9 ).