homology packages and LocusLink IDs

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Lynn Young ▴ 30

@lynn-young-279

Last seen 10.2 years ago

Greetings, In the vignette, "How to use the homology packages" under Task 1, what is the recommended method of obtaining the LocusLink IDs of the homologous genes? Sincerely, Lynn Young

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ADD COMMENT • link updated 19.6 years ago by rgentleman ★ 5.5k • written 19.6 years ago by Lynn Young ▴ 30

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rgentleman ★ 5.5k

@rgentleman-7725

Last seen 9.6 years ago

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Hi Lynn, I am not sure quite what you are asking - the point of that part of the vignette is to explain how to map from LocusLink (soon to be Entrez Gene) IDs to other things. Typically you have Entrez IDs for other reasons - like from an analysis of differential expression, or by choosing a particular GO term and finding the associated genes or, perhaps mapping an analysis done on one species to another; pretty much the list is endless. Or are you asking about mapping from Entrez gene ID one to a homologous gene, and for that gene you want to get the Entrez Gene ID? In that case, right now, you would get the homology environment for the appropriate (second) species and use its homologene ID to map to the Entrez Gene ID for that species. I believe that this will be changing in the next release (any day now), as Homologene has really changed their data formats and keys, and seem to be relying more on Entrez IDs and less on Homologene IDs. They also seem to have substantially expanded the information available (and contracted the number of species it is available for) we will be trying to enhance the packages, but any suggestions or requests would be quite welcome. Regards, Robert On May 13, 2005, at 11:33 AM, Lynn Young wrote: > Greetings, > > In the vignette, "How to use the homology packages" under Task 1, what > is the recommended method of obtaining the LocusLink IDs of the > homologous genes? > > Sincerely, > Lynn Young > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > +--------------------------------------------------------------------- -- ----------------+ | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: rgentlem@fhcrc.org | +--------------------------------------------------------------------- -- ----------------+

ADD COMMENT • link 19.6 years ago rgentleman ★ 5.5k

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Hi Robert, Thanks for the response. Congratulations on your new position! Yes, my question is once I get a list of homologene IDs back from the homology environment, is there a simple way to map them to a gene ID. The homoLL example doesn't seem to work. I can wait for the next release and try again, if you like. Warmly, Lynn On May 14, 2005, at 1:51 PM, Robert Gentleman wrote: ... ??? Or are you asking about mapping from Entrez gene ID one to a? homologous gene, and for that gene you want to get the Entrez Gene ID?? In that case, right now, you would get the homology environment for the? appropriate (second) species and use its homologene ID to map to the? Entrez Gene ID for that species. I believe that this will be changing in the next release (any day now),? as Homologene has really changed their data formats and keys, and seem? to be relying more on Entrez IDs and less on Homologene IDs. They also? seem to have substantially expanded the information available (and? contracted the number of species it is available for) we will be trying? to enhance the packages, but any suggestions or requests would be quite? welcome. Regards, ? Robert On May 13, 2005, at 11:33 AM, Lynn Young wrote: > Greetings, > > In the vignette, "How to use the homology packages" under Task 1, what > is the recommended method of obtaining the LocusLink IDs of the > homologous genes? > > Sincerely, > Lynn Young Lynn Young, PhD * National Institutes of Health, USA CIT, MSC 5624; Bethesda, Maryland 20892-5624 Phone: (301) 496-1137 * FAX: (301) 402-4544 E-mail: lynny@mail.nih.gov

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