Subject: Helping FlyBase: ADRC-60024 Dear Stuart, We are currently curating the abstracts for the upcoming 48th (Philadelphia) Annual Drosophila Research Conference, for FlyBase. I am writing in connection with your abstract: dSno facilitates Baboon signaling in the Drosophila brain by switching the affinity of Medea away from Mad and toward dSmad2. You mention a gene that is new to FlyBase, 'dSno'. We'd drop the d for Drosophila in this symbol as we name the gene record - but it is clear that this is a known gene. Are you able to tell us which CG it corresponds to? We do already have a gene called sno (strawberry notch) so introducing a Sno will be potentially confusing, and will produce unhelpful double hits in certain on-line searches. Would you be willing to consider a more distinct symbol - such as Snonc? Best regards, Rachel. Subject: RE: Helping FlyBase: ADRC-60024 Hi Rachel, Thanks for your note. I knew this would be an issue. Might as well tackle it now. The dSno gene is CG7233 plus the adjacent CG7093. Currently CG7233 is called SnoN in Flybase. However, I do not think it's feasible to simply rename dSno to SnoN because SnoN is the name of one protein isoform generated by the dSno locus - the other isoforms are SnoA, SnoI and SnoN2. This nomenclature follows precedents derived from a large literature on mammalian Sno alternative transcripts and protein isoforms. You can read all about this complicated gene, its misprediction and multiple proteins (and even more transcripts) in my paper - the cover story of the November 2006 issue of Genetics - Takaesu et al. I am willing to listen to suggestions that simplify things in Flybase but in considering any name changes I must keep in mind that many investigators interested in this particular gene are from other systems who may never encounter confusion with strawberry notch. A lesser worry, but something that still needs to be kept in mind, are 6 dSno cDNA sequences in Genback. These were released back in June with the name of the relevant dSno isoform and variant promoter. The accesion numbers are in the paper. Let me know what you think after looking at the paper. If you will be in Philly next week we could talk in more detail - I am presenting the dSno story on Saturday morning. Best, Stuart Subject: RE: Helping FlyBase: ADRC-60024 Hi Stuart, Sorry to take so long to get to this. Your Genetics paper has in fact been curated (nice front cover) - ready for next FB update. The gene symbol in FlyBase is currently snoN. I see why you find this problematic, given SnoA, SnoI and SnoN2. > I am willing to listen to suggestions that simplify things in Flybase but in considering any name changes I must keep in mind that many investigators interested in this particular gene are from other systems who may never encounter confusion with strawberry notch. Indeed they may not. So are you advocating Sno as a better symbol for snoN:FBgn0031967 ? Despite the inevitable confusion (searches, mistaken cross-links) with strawberry notch? We can do this, if you insist, though you should be (probably already are) aware that people who care about nomenclature (Kevin, Scott) have suggested that we should not confer gene symbols that differ only from other symbols by case, and were that to be enforced then your Sno may have to change (as sno:strawberry notch, FBgn0005410, has clear precedence). This is why I suggest Snonc, or Sno-onc, for clarity. In terms of papers and presentations, once you have identified that your work is regarding 'Snonc', or 'Sno-onc', then you can always use the 'abbreviated as Sno throughout' manouvre. As a consequence of your Genetics paper being curated, it will be getting the full name 'Sno oncogene', so either of those suggestions makes sense. I'm guessing you don't like them particularly, or else you would have picked them up in response to my first, but I am of course happy to check out any other suggestion you might have. So let me know whether or not you are insisting on Sno, or whether you want me to check out other possibiltities, and I'll make the ADRC and Genetic paper curation consistant with respect to each other. Enjoy the conference - good luck with the talk. my best, Rachel. Subject: RE: Helping FlyBase: ADRC-60024 Hi Rachel, I did not notice any delay and thanks for your informative note. I am sensitive to the issue of gene names separated solely by capitals and am not considering that. I have two thoughts on abbreviations that are along the lines of your proposed Snonc, or Sno-onc. I was unaware that these were designed to be consistent with the curation of my paper in Flybase (and thanks for the kinds words about our cover). First how about - SnoO or Snoo? This certainly fits with the formal Flybase name Sno-oncogene The last letter can be capitalized or not D. The consideration here is that this is a gene name and other Sno names with last letters capitalized correspond to protein isoforms, though no isoform exists with this particular name. Second, how about Snow? The final w (lower case) creates a cute abbreviation that maintains the genes unique identity. This fits perhaps a bit better with the mammalian nomenclature as Ski is a related gene in mammals but one that does not have a fly homolog (see fig. 1 of our paper). Of the two, I favor the latter but certainly understand if database or other considerations lead Flybase to choose the former or one of your suggestions. Sorry to be making your job that much harder than it already is. Regards, Stuart Subject: RE: Helping FlyBase: ADRC-60024 Hi Stuart, great! the good news is that SnoO Snoo and Snow are all available - un-used for anything else perhaps I am being dim (!) but I don't see where the w in Snow comes from - unless its just for the pronunciation my personal fave is Snoo - but its your choice so let me know and I'll make it so > I was unaware that these were designed to be consistent with the curation of my paper in Flybase oh yes - its all about keeping things together when they should be (and not when they should not) my best Rachel. Subject: RE: Helping FlyBase: ADRC-60024 Rachel - your favorite fits fine with me - Let's make it Snoo. Regards Stuart
