Gene id to gene name mapping

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7.8 years ago

GR ▴ 400

Hi All,

Can anyone suggest a way to extract gene Id to gene names mapping for A. thaliana.

Thanks, RT

gene id gene name • 3.3k views

ADD COMMENT • link 7.8 years ago by GR ▴ 400

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Do you mean to extract the gene IDs corresponding to a set of gene names?

ADD REPLY • link 7.8 years ago by iraun 6.2k

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I need it for all the A thaliana genes. For example,

Geneid | Genename |

AT4G21690.1 | GA3OX3 |

ADD REPLY • link 7.8 years ago by GR ▴ 400

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You can use BioMart. Just give as input a list of arabidopsis gene IDs or gene names, and for the output you can select "Gene stable ID" and "Gene name" attributes. Is this what are you looking for?

ADD REPLY • link 7.8 years ago by iraun 6.2k

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If you're working in R, you can use BioMartR. We have been very successful with it. However, there are a few times when the service (on the BioMart end) might be running slow or be unavailable, so make sure to account for that vs. thinking your R script has an error.

ADD REPLY • link 7.8 years ago by JP ▴ 30

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