Fig. 5.

TF regulatory networks from XL-DNase-seq have reproducible connections as well as new connections. a De novo construction of transcriptional regulatory networks. FDR 1% footprints within 5 kb of TSSs were used to obtain regulatory relationships. b TF regulatory network derived from 0.1% formaldehyde 10 min XL-DNase-seq data (MS5 and MS11, merged) after correcting for the dimer bias of DNase. Regulatory connections which were also detected in the network from native DNase-seq are marked in blue. See also Additional file 2: Fig. S8