Illustration of the flow of information in regulatory region annotation. Given a coexpressed group of genes, one can use (a) motif discovery or (b) search for known motifs in the upstream regions (motif building). Weight matrices can be used to scan sequences in a variety of ways: (c) the sites predicted by scanning the mouse Hspa1b promoter with the TRANSFAC matrix M01023 (left) and the conservation of those sites in vertebrate promoters (right).
Vingron et al. Genome Biology 2009 10:202 doi:10.1186/gb-2009-10-1-202