I am trying to perform motif analysis on the promoters of a set of human genes known to be pro-inflammatory, many Nfkb and CEBPb targets. I tried several tools, MEMECHIP (and other MEME tools), Homer, RSAT and I don't see any Nfkb or CEBPB enrichment.
Then I tried a set of peaks obtained with CEBPb ChIP-seq and again i did not obtain any enrichment for CEBPB. I also tried a short (< 100) gene list known to be canonical Nfkb targets and again, failed to get any RELA related enrichment. Many SP1-3 come up so then I tried enhancer peaks (defined separately) and again failed to get any inflammation-related motif enrichment.
I also tried different representations of promoters/enhancers e.g. TSS +- 500, 1500, 2500 or just nucleosome-free regions in the promoter/enhancers. Please offer any advice on how you do motif enrichment analysis.
Thank you in advance!