

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
>> 
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> 
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