Chunk #8 — INTRODUCTION — Improved hidden Markov Models and phylogenetic trees, and ortholog identification — Orthologs: identification of complete set of orthologs and best one-to-one (least diverged) ortholog
These improved gene trees provide the basis for accurate inference of orthologs, pairs of genes whose most recent common ancestor (MRCA) diverged due to a speciation event (8). Orthologs of each gene can be viewed on PANTHER gene pages, and the entire set of pairwise ortholog inferences can be downloaded from the PANTHER website (http://www.pantherdb.org/downloads). For orthologs, PANTHER reports not only one-to-one but also one-to-many (i.e. when gene duplication has occurred in one lineage following speciation) and many-to-many orthologs (i.e. when gene duplication has occurred in both lineages following speciation). In the case of multiple orthologs, PANTHER identifies the one-to-one relationship that has ‘diverged the least’ following any gene duplication events. The ‘least diverged ortholog’ (LDO) pairs therefore represent the most nearly ‘equivalent’ gene pairs between different organisms based on the phylogenetic tree. Following gene duplication, the most common fates of the copies are thought to be neofunctionalization (in which one copy retains the ancestral function, while the other adapts to a new function) and subfunctionalization (in which each copy specializes in a subset of the ancestral functions) (9). If
