Probabilistic functional gene societies

A cellular system may be viewed as a social network of genes. Genes work together to conduct physiological processes in the cells. Thus if we have a view of the functional association among genes, we may also be able to unravel the association between genotypes and phenotypes; the emergent properties of interactive activities of genes. We could have various points of view for a gene network. Perhaps the most common standpoints are protein–protein interaction networks (PPIN) and transcriptional regulatory networks (TRN). Here I introduce another type of view for the gene network; the probabilistic functional gene network (PFGN). A ‘functional view’ of association between genes enables us to have a holistic model of the gene society. A ‘probabilistic view’ makes the model of gene associations derived from noisy high-throughput data more robust. In addition, the dynamics of gene association may be presented in a single static network model by the probabilistic view. By combining the two modeling views, the probabilistic functional gene networks have been constructed for various organisms and proved to be highly useful in generating novel biological hypotheses not only for simple unicellular microbes, but also for highly complex multicellular animals and plants.