Phylogenetic profiling

Phylogenetic profiles describe the presence or absence of a protein in a set of reference genomes. Similarity between profiles is an indicator of functional coupling between gene products: the greater the similarity, the greater the likelihood of proteins sharing membership in the same pathway or cellular system. By virtue of this property, uncharacterized proteins can be assigned putative functions, based on the similarity of their profiles with those of known proteins. Profile comparisons, when extended to the entire genome, have the power to reveal functional linkages on a genome-wide scale (the functional "interactome"), elucidating both known and novel pathways and cellular systems.