Hi Peng, It seems that the homologene.data file at NCBI is clearly ad hoc ftp://ftp.ncbi.nih.gov /pub/HomoloGene/current/homologene.data 3 9606 34 ACADM 187960098 NP_001120800.1 3 9598 469356 ACADM 160961497 NP_001104286.1 3 9615 490207 ACADM 73960161 XP_547328.2 3 9913 505968 ACADM 115497690 NP_001068703.1 3 10090 11364 Acadm 6680618 NP_031408.1 3 10116 24158 Acadm 8392833 NP_058682.1 3 7955 406283 acadm 47085823 NP_998254.1 3 7227 38864 CG12262 24660351 NP_648149.1 3 7165 1276346 AgaP_AGAP005662 58387602 XP_315683.2 3 6239 181757 acdh-10 17569725 NP_510788.1 3 6239 173979 acdh-8 17534899 NP_495142.1 3 6239 181758 acdh-7 17570075 NP_510789.1 3 9544 705168 ACADM 109008499 XP_001101187.1 5 9606 37 ACADVL 4557235 NP_000009.1 5 9598 455237 LOC455237 332847152 XP_003315394.1 5 9615 489463 ACADVL 345800108 XP_546581.3 with 9606 for human, 10090 for mouse ... and the same value in column 1 for the same gene Best regards Philippe Dessen IGR, Villejuif, france Le 30 juil. 2012 à 19:28, Marc Carlson a écrit : > Hi Peng, > > Yes it's a fact of life that inparanoid has not updated their data for a while. It's pretty likely however that a lot of what you care about will not have changed appreciably. Especially if you are comparing gene to gene mappings between human and mouse. Another resource that you can look at for mouse to human gene to gene mappings is homologene. There is not currently an annotation package for homologene although I have almost made one on several occasions. > > Also, I think that the ensembl biomaRts also have homology information, so you could also use the biomaRt package if you are not a fan of inparanoid. > > > Marc > > > > On 07/26/2012 03:14 PM, Peng Yu wrote: >> Hi, >> >> I'm wondering to how updated hom.Hs.inp.db is. >> >> "Title: Homology information for Homo Sapiens from Inparanoid" >> >> According to the title of the package, the data is from Inparanoid. >> However, when I check http://inparanoid.sbc.su.se/cgi- bin/index.cgi, >> it says "Version 7.0, Updated June 2009 (release notes)". It seems to >> me that the data in Inparanoid is not very updated? In this case, if I >> want to get the reasonably updated symbol mapping between human and >> mouse, is it better to just to go ncbi, or is there a more convenient >> alternative? (BTW, I also see something in the vignette of >> annotationTools, not sure if this is the best way.) >> >> Thanks! >> >> -- >> Regards, >> Peng >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]