Transcription factors possess both, ability to activate genes and ability to repress genes. Some transcription factors act as repressor for some genes and activators for others. I am looking for experimental evidence for transcription factors that are known to act as repressor for some genes and others which are known to act as activators. I was wondering if there is a curated list of genes which are activated by some transcription factors and similarly a list of genes repressed by a that particular transcription factor. Where can I find such information other than mining literature for the same.
2 answers
One way to find out what you want would be to:
- Get the gene_association.goa_human (http://www.geneontology.org/gene-associations/)
- Parse terms "repressor" or "activator" or similar
cat gene_association.goa_human | grep "repressor" | wc -l # 692
cat gene_association.goa_human | grep "activator" | wc -l # 3545
cat gene_association.goa_human | grep "Transcriptional activator" | wc -l # 274
column 3 will be your gene list, you can play with the grep terms to get more specific or more general results
-- edit --
Just realized that you want to know which regulator activates/represses which gene...
To go around it you could use the gene list you got from up and parse the MSigDB signatures
The ENCODE chip seq significance tool gives you a list of TF that bind based on your target gene list
STRING allows you to select the "action" button and that will show you activation or repression
..so I feel you need to do some hopping around to get a specific answer
Take a look at this gene regulatory network, we found some genes that seem to increase expression of others, and some genes that seem to decrease expression of others. The supplemental data tables have lists of mouse genes.
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0100842
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karl.stamm
So is this type of list only meant for Cardiologic tissues or is it ok to use this list for other tissues. What I am looking for is a general rule for all Human and/or Mouse transcription factor. i.e. which genes they activate and which ones they repress. I am doing a large scale study so would need this kind of information for all Human and Mouse transcription factor across all tissues.
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You want information other than mining the literature?
I don't want to reinvent the wheel. So if somebody has a curated list for the same I would be happy to use it.
Since phenomenon like these have been well described in the review papers I am assuming this kind of information does exist but I don't know where and how to find it.