UNLABELLED: We introduce the Protein Link EXplorer (PLEX), a web-based environment that allows the construction of a phylogenetic profile for any given amino acid sequence, and its comparison with profiles of approximately 350,000 predicted genes from 89 genomes, as a means of interactively identifying functionally linked genes and predicting protein function. PLEX can be searched iteratively and also enables searches for chromosomal gene neighbors and Rosetta Stone linkages. PLEX search results are accompanied by quantitative estimates of linkage confidence, enabling users to take advantage of coinheritance, operon and gene fusion-based methods for inferring gene function and reconstructing cellular systems and pathways. AVAILABILITY: http://bioinformatics.icmb.utexas.edu/plex

The amount of data produced by molecular biologists is growing at an exponential rate. Some of the fastest growing sets of data are measurements of gene expression, comparable in quantity only to gene sequences and the vast biological literature. Both gene expression data and sequence data offer hints as to the functions of thousands of newly discovered genes, but neither give complete answers. Therefore, much effort is being focused on integrating these large data sets and combining them with all available functional data to draw inferences about the functions of uncharacterised genes. This review discusses the most pertinent functional data for genome-wide functional inference and describes several methods by which these disparate data types are being integrated.