Cyclophilin nomenclature problems, or, 'a visit from the sequence police'

Abstract

Abstract Why is agreement on one particular name for each gene important? As one genome after another becomes sequenced, it is imperative to consider the complexity of genes, genetic architecture, gene expression, gene-gene and gene-product interactions and evolutionary relatedness across species. To agree on a particular gene name not only makes one's own research easier, it aids automated text-mining algorithms and search engines, which are increasingly employed to find relationships in the millions of abstracts in the medical research literature and sequence databases. A common nomenclature system will also be helpful to the present generation, as well as future generations, of graduate students and postdoctoral fellows who are about to enter genomics research. In this paper, the authors present some problems that arose when two separate research communities decided to choose the same root, CYP, for naming their gene families. They then offer a logical solution, by renaming the cyclophilin genes with a common root, such a cyn- in Caenorhabditis and CYN- in mammals (Cyn in mouse), and using evolutionary divergence to cluster genes of the highest level of relatedness.

Keywords

• human genome
• mouse genome
• Caenorhabditis elegans genome
• cytochrome P450 (CYP) gene superfamily
• cyclophilin gene family
• immunophilins
• peptidylprolyl cis-trans isomerases
• FK506-binding proteins
• tacrolimus
• parvulin