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How To Convert Arabidopsis Gene Id To Ncbi Geneid, Ncbi-Gi Or Uniprot?
Hi all, I have a list of Arabidopsis Gene ID and want to get pathway analysis in KEGG(http://www.genome.jp/kegg/kegg2.html). Since only NCBI GeneID, NCBI-gi and UniProt is accessible KEGG GENES Entry Name, I want a method to convert Arabidopsis Gene ID to NCBI GeneID, NCBI-gi or UniProt.
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Hi!
You can also download the file: ftp://ftp.ncbi.nih.gov/gene/DATA/gene_info.gz
A row in that file looks like:
3702 836056 ACT4 AT5G59370 F2O15.3|F2O15_3|actin 4 TAIR:AT5G59370 5 - actin 4 protein-coding - - - - 20110531
First column: taxonomy ID Second column: Entrez gene ID Fourth column: gene name Fifth column: description
It should be fairly easy to write a program that picks up either on the content of the fourth column and returns the Entrez gene id. Alternatively, you can also look for the prefix "TAIR:" in the description and then match the following id.
Joachim
id mapping facility at http://www.uniprot.org/ may be helpful for you
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What do your Arabidopsis Gene ID look like ? From what database is it coming from ?
For example: AT5G59370 AT4G37770 AT4G33090 AT4G09650 AT1G61820 AT4G24890 AT2G35040 AT5G06100
This should work for you; http://bit.ly/pEq7LO. Just look for the specific IDs you need from the guide.
It's always a good idea to try Biomart. Version for plants: http://www.gramene.org/biomart/martview/ea115ee510b63cb6b1680c47ebec3440