Cyclophilin nomenclature problems, or, 'a visit from the sequence police'
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Cyclophilin nomenclature problems, or, ‘a visit from the sequence police’ Daniel W. Nebert,1* Nickolas A. Sophos,2 Vasilis Vasiliou2 and David R. Nelson3 1
Department of Environmental Health and Center for Environmental Genetics (CEG), University of Cincinnati Medical Center, Cincinnati, OH 45267-0056, USA 2 Molecular Toxicology and Environmental Health Sciences Program, Department of Pharmaceutical Sciences, University of Colorado Health Sciences Center, Denver, CO 80262, USA 3 Department of Molecular Sciences and The UT Center of Excellence in Genomics and Bioinformatics, University of Tennessee, Memphis, TN 38163, USA *Correspondence to: Tel: þ1 513 558 4347; Fax: þ1 513 558 3562; E-mail: [email protected] Date received (in revised form): 4th May 2004
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 textmining 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 as 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
Introduction A previous paper in this series1 summarised the steps that one is strongly encouraged to follow in order to ensure proper nomenclature of any gene. Three examples were given to illustrate how and why one should strive for a standardised gene nomenclature system. In these examples, the focus of the paper was on using the gene names as search terms, rather than comparing a DNA or protein sequence that has just been determined by searching via BLAST.2 The three examples included: PTGS1 and PTGS2 as the correct gene names for prostaglandin G/H synthase-1 and -2, also known as cyclooxygenase-1 and -2 and commonly erroneously nicknamed ‘COX-1’ and ‘COX-2’ in many journals; the short- and long-chain fatty acid synthase gene families, for which there is currently no official agreed-upon nomenclature (although FASN on human chromosome 17q25 is the official symbo
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