Using genomic DNaseI footprinting33,34 on 41 cell types we identified 8.4 million distinct DNaseI footprints (FDR 1%)25. Our de novo motif discovery on DNaseI footprints recovered ~90% of known TF motifs, together with hundreds of novel evolutionarily conserved motifs, many displaying highly cell-selective occupancy patterns similar to major developmental and tissue-specific regulators.
