Dear Sir,


Could you tell me if there are any mapping file for cochloroplast or mitochondiron encoded genes, particularly, for Arabidopsis ? If possible, where can I get it? Sorry for bothering you if my question is not clear.

Sincerely,

Yuqing

Department of Microbiology and Cell Science
University of Florida

Hi Yuqing,

chloroplast and mitochondrial genes are actually included in the AGI-code
based mapping that we provide for Arabidopsis (codes starting with "AtCg"
or "AtMg".

I hope this answers your question.
Best greetings,
Marc

Hi, Marc,

Thanks a lot for your prompt reply. Actually I tried with my dataset which include chloroplast genes, but no any chloroplast genes can be mapped. As you said, chloroplast genes starts with "AtCg". my data, however, start with "ArthCp". I thought this This is probably the reason. So I changed the name of each gene from, for example, ArthCp009 to AtCg009. But it still show me the below info. Can you tell what the problem could be?

**********************************************************************************
Data does not fit mapping used
(No data points mapped)!
Please choose the appropriate mapping which matches your data!
**********************************************************************************

Thanks a lot!

Yuqing

Hi Yuqing,

as i said previously, the arabidopsis mapping that we supply is based on AGI Locus IDs as published
by TAIR (http://www.arabidopsis.org/). The IDs you are working with seem to be KEGG IDs. To be able
to work with the MapMan mapping these KEGG IDs would first have to be translated to their corresponding
AGI IDs. It is, unfortunately, not sufficient to simply replace the "ArthCp" part by "AtCG".

In the case of the gene you used as an example (ArthCp009) the corresponding AGI code would be AtCg00140.
Most of the KEGG entries seem to contain a crossreference to the AGI code - However not all of them do.
It seems like the KEGG site is not offering a nice bullk crossmapping service but maybe i just did not see it.
All the mitochondrial and chloroplast genes are listed at the end of this very long list of genes in the KEGG DB.
It seems like they stuck to the AGI identifiers for nuclear genes but use a different nomenclature for organellar
genes which makes is complicated for us. In the worst case, this would make it necessary to manually find
the AGI codes corresponding to all the organellar KEGG codes by clicking through all the entries in KEGG.

I've been looking for a better solution for the last hour, but no success - sorry for not being able to provide a
better suggestion. I guess the information you need would be available from the KEGG FTP server, however
access to this is not completely free (http://www.kegg.jp/kegg/download/) - at least you'd have to subscribe
individually as an academic user.

cheers,
Marc

Hi, Marc

I really appreciate your help. I figured out the problem. It is exactly like what you said. Fortunately, there are no too many chloroplast-encoded genes. so I manually converted the name. And I also would like to mention that some names have no cross-reference to the AGI code. I just used the localization information (bp) or sequence blast, and easily and accurately find the AGI code. Thanks again for your nice help.

Best,

Yuqing