A probabilistic functional gene network for baker's yeast, Saccharomyces cerevisiae, which has been a major model organism for eukaryotic genetics and cell biology. YeastNet v3 provides a new web interface to run the tools for network-guided hypothesis generations. YeastNet v3 also provides edge information for all data-specific networks (approximately 2 million functional links) as well as the integrated networks. Therefore, users can construct alternative versions of the integrated network by applying their own data integration algorithm to the same data-specific links.