Question: To find the genes encoding for Transcription factor in a given list
0
gravatar for siddhu16
14 months ago by
siddhu160
siddhu160 wrote:

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.

genome sequence R gene • 442 views
ADD COMMENTlink written 14 months ago by siddhu160
2
gravatar for michael.ante
14 months ago by
michael.ante3.6k
Austria/Vienna
michael.ante3.6k wrote:

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.

ADD COMMENTlink modified 14 months ago • written 14 months ago by michael.ante3.6k

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.

ADD REPLYlink modified 14 months ago • written 14 months ago by Emily_Ensembl20k
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