To find the genes encoding for Transcription factor in a given list

Question

[siddhu16]

Hi all, I have a list of about 500 genes (of Arabidopsis thaliana) with their Entrez ID, in that, I have to find which genes codes for a transcription factor. Is there any tool to perform this analysis.

Answer 1

[michael.ante]

I'd go for ENSEMBL's biomart and extract the genes and their GO term. In the resulting file, you may look for the GO term for "transcription factor activity". Maybe you can also do it via R and some biocinductor packages.

[EDIT] The R/bioconductor package would be biomaRt and here is a description how to use the plants' biomart.

[Emily]

To make it even easier, filter by 'go_parent_term' and the term listed above. That will get you all genes associated with that and any child terms of that.