The main goal of PANTHER is to infer the evolution of gene function across as many genes in as many genomes as possible, and apply these inferences to predict the functions of genes that have not been directly characterized by experiment. In particular, there are large communities of researchers elucidating gene function for so-called ‘model organisms’ (e.g. those listed in Table 1) and these results provide a basis for inferring the functions of related genes in humans and other organisms. PANTHER applies both software tools and manual curation to perform these inferences as accurately as possible, and to keep them up-to-date as new experimental results accumulate. Gene function—or, more commonly, the function of gene products such as proteins—is described using terms from the Gene ontology (GO) (3,4), or from representations of molecular pathways. Table 1.Sources for complete sets of protein-coding genes in PANTHER version 7Organism or clade(s)Five-letter codeData sourceReferenceArabidopsis thalianaARATHTAIR(11) Dicot plantCaenorhabditis elegansCAEELWormBase(12) Nematode wormDanio rerioDANREEnsembl, ZFIN(13) ZebrafishDictyostelium discoideumDICDIDictyBase(14) Cellular slime moldDrosophila melanogasterDROMEFlyBase(15) Fruit flyEscherichia coliECOLIEcoCyc(16) BacteriumGallus gallusCHICKEntrez Gene(17) ChickenHomo sapiensHUMANSwissProt(18) HumanMus musculusMOUSEMGI(19) MouseRattus norvegicusRATRGD(20) RatSaccharomyces cerevisiaeYEASTSGD(21) Budding yeastSchizosaccharomyces pombeSCHPOGeneDB(22) Fission yeastOther chordate genomesEnsembl(23)Other non-chordate genomesEntrez Gene(17)
