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.
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.
You can use the following converter.
You've got to paste you list on the left and select the TAIR id from the drop down on the left and decide what you want it to convert to on the right. It's quite useful.
Hope that helps.