Uncovering trends in gene naming

Abstract

We take stock of current genetic nomenclature and attempt to organize strange and notable gene names. We categorize, for instance, those that involve a naming system transferred from another context (for example, Pavlov's dogs). We hope this analysis provides clues to better steer gene naming in the future.

Figure 1

Criteria and examples of gene name classification. ^aSEMA5A (human): sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A; ^bdrop dead (Drosophila): flies with mutations in drop dead die rapidly after their brain rapidly deteriorates. ^cmalvolio (Drosophila): gene needed for normal taste behaviour. Malvolio in Shakespeare's Twelfth Night tasted "with distempered appetite". ^dLOV (many different organisms): light, oxygen, or voltage (LOV) family of blue-light photoreceptor domains. ^eyuri (Drosophila): this gene was discovered on the anniversary of Yuri Gagarin's space flight. Mutants have problems with gravitaxis and cannot stay aloft. ^ftribbles (Drosophila): cells divide uncontrollably, like the eponymous Star Trek characters. ^gkuzbanian (Drosophila): mutants have uncontrollable bristle growth. Koozbanians are alien Muppets with uncontrollable hair growth; spelling was changed to avoid copyright infringement. ^hring (Drosophila): really interesting new gene. ⁱyippee (Drosophila): a graduate student's reaction on cloning the gene. ^jkryptonite and superman (Arabidopsis): the kryptonite mutation suppresses the function of the SUPERMAN gene. ^karleekin, valient, tungus (Drosophila): mutations in arleekin, valient, tungus and 29 other genes affect long-term memory. Named after Pavlov's dogs. ^lPKD1 (human) and lov-1 (worm): these are homologs, although their names do not suggest it. ^mMT-1 (human): this label can refer to at least 11 different human genes. ⁿBAF45 and BAF47 (mouse): names for the same gene, reflecting a revision of the molecular weight of product.

Figure 2

Comparisons of gene names. (a) Schematic of 'skewed' gene names inter-species comparison. Horizontal axis, Web search results for gene name using Yahoo! search engine. Vertical axis, search results using gene name as PubMed query. Overlapping ovals, predicted name distribution for S. cerevisiae (green), E. coli (blue) and D. melanogaster (red) based on naming systems employed in these species. (b) 'Skewed' gene names inter-species comparison. Actual name distribution for S. cerevisiae (green), E. coli (blue) and D. melanogaster (red). H. influenzae is not shown; the strict, identifier-style names in this species generated virtually no Web hits, so these names appeared entirely along the base of the horizontal axis and were omitted.