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?
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).