Is there any tools to detect enrichment of transcription factor targets from microarray/RNAseq data. I have heard that Metacore has this functionality, but is there a freely available mapping of transcription factors to targets that could be queried in a way analogous to the way DAVID or GOseq queries GO/KEGG pathway enrichment?
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Dave Bridges
What I would do is to look at the overrepresentation of TF binding profile motifs in the promoter sequences of your target genes. I did it several times with success. You could use the oPOSSUM3 webtool for instance by providing a list of genes and it will look for overrepresented TFBSs in their promoter sequences. You just need to be really careful with the background sequences you use.
DAVID (http://david.abcc.ncifcrf.gov/summary.jsp) can actually perform TFBS enrichment. After uploading a gene list, see the Chart for "UCSC TFBS" under "Protein Interactions", which will show you over-represented TFBS within your gene list as compared to your background list (or the entire genome if none is provided).
It doesn't seem to have this function now! If anyone knows any alternative, that'd be extremely useful!
It doesn't seem to have this function now! If anyone knows any alternative, that'd be extremely useful!
I thought they did a similar thing in the ENCODE project for humans. Maybe check that out: http://www.ncbi.nlm.nih.gov/pubmed/22955984/
For plants, you can try PlantRegMap to find the enriched transcription factors in a set of genes.
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