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

Table 5

Main features of the types of bioinformatics tools used for the analysis of DNA microarray data.

Tools and resources	Goal	Methods
Class level functional Annotation	Determine a biological meaning to groups of related genes identified by microarray analysis	Overrepresentation test of gene ontology (GO) terms
Gene coexpression	Identify common expression patterns between genes in order to infer biological function	Correlation tests of gene expression
Gene network Analysis	Capture the interconnectedness of cellular components in order to explain biological phenomena	Systems biology approach
Gene network reconstruction	Develop models for gene regulatory networks	Bayesian inference theory Mutual information theory
Network visualization	Display a simplified view of large amount biological components and their interactions	Graph theory
Network exploration	Associate network nodes and edges with biological information	Incorporate heterogeneous data from various databases
Biological pathway resources	Map biological pathways information into inferred network	Collect and process information from pathway databases
Transcriptional regulation analysis	Identify transcription factors that regulate gene expression	Overrepresentation test of regulatory motifs in promoter regions of related genes