How To Convert Arabidopsis Gene Id To Ncbi Geneid, Ncbi-Gi Or Uniprot?

Question

[Wutomg]

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.

[boczniak767]

It's always a good idea to try Biomart. Version for plants: http://www.gramene.org/biomart/martview/ea115ee510b63cb6b1680c47ebec3440

[Pasta]

What do your Arabidopsis Gene ID look like ? From what database is it coming from ?

[Wutomg]

For example: AT5G59370 AT4G37770 AT4G33090 AT4G09650 AT1G61820 AT4G24890 AT2G35040 AT5G06100

[Yogesh Pandit]

This should work for you; http://bit.ly/pEq7LO. Just look for the specific IDs you need from the guide.

Answer 1

[Joachim]

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

Answer 2

[Hranjeev]

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.

[Boboppie]

DAVID is helpful ;)

[Hranjeev]

However I heard the database in DAVID may not be up to date so you may want to validate your list via the other method I listed.

Answer 3

[Hranjeev]

The following link is also useful to convert the TAIR ids you specified.

Answer 4

[Palu]

id mapping facility at http://www.uniprot.org/ may be helpful for you