Fig. 1

BROCKMAN. a The relationship between the differential activity of TFs that open chromatin and the numbers of their cognate motifs associated with open chromatin. Shown is a cartoon example of the impact of TFs (circles) on chromatin accessibility when the TF’s concentration is low (left) or high (right), for different scenarios of TFs that can (top and bottom rows) or cannot (middle row) open chromatin. If the TF can open chromatin either alone (top) or cooperatively (bottom), a change in the concentration or activity of TFs will affect the number of accessible binding sites in the cell (colored bars). If a TF has no effect on accessibility (middle), there will be no relationship between accessible motifs (bars) and the TF’s concentration. b BROCKMAN method. From left: genomic sequences associated with open chromatin or another feature of interest are used as input (left), and the frequency of each k-mer in open chromatin/feature (row) is counted in each sample (column) (middle), the resulting k-mer frequency matrix is then decomposed by PCA (right) into the k-mers contributing to each PC (left matrix) and the projection of the samples into the new (PC) space (right matrix)