This is a test version of Biostars. For the public version, visit https://www.biostars.org.
To find the genes encoding for Transcription factor in a given list

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.

gene r genome sequence
• 1,753 views • link
written by siddhu16 • siddhu16

1 answer

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.

• 1 views • link
written by michael.ante michael.ante

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.

• 1 views • link
written by Emily Emily

Log in to answer this question.

More posts like this