Question: How To Convert Arabidopsis Gene Id To Ncbi Geneid, Ncbi-Gi Or Uniprot?
2
gravatar for Wutomg
8.3 years ago by
Wutomg20
Wutomg20 wrote:

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.

mapping identifiers • 12k views
ADD COMMENTlink modified 8.1 years ago by Palu170 • written 8.3 years ago by Wutomg20

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

ADD REPLYlink written 8.3 years ago by Pasta1.3k

For example: AT5G59370 AT4G37770 AT4G33090 AT4G09650 AT1G61820 AT4G24890 AT2G35040 AT5G06100

ADD REPLYlink written 8.3 years ago by Wutomg20

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

ADD REPLYlink written 8.1 years ago by Yogesh Pandit500

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

ADD REPLYlink written 7.8 years ago by boczniak767640
2
gravatar for Joachim
8.3 years ago by
Joachim2.8k
San Francisco, California
Joachim2.8k wrote:

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

ADD COMMENTlink written 8.3 years ago by Joachim2.8k
1
gravatar for Hranjeev
8.3 years ago by
Hranjeev1.5k
Malaysia
Hranjeev1.5k wrote:

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.

ADD COMMENTlink written 8.3 years ago by Hranjeev1.5k

DAVID is helpful ;)

ADD REPLYlink written 8.3 years ago by Boboppie530

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.

ADD REPLYlink written 8.3 years ago by Hranjeev1.5k
1
gravatar for Hranjeev
8.3 years ago by
Hranjeev1.5k
Malaysia
Hranjeev1.5k wrote:

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

ADD COMMENTlink written 8.3 years ago by Hranjeev1.5k
0
gravatar for Palu
8.3 years ago by
Palu170
Palu170 wrote:

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

ADD COMMENTlink written 8.3 years ago by Palu170
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