Fig. 6

Two clusters from the ENCODE-motif dataset, with edge thickness representing the co-occurrence frequency edge weight generated by our method, and edge color (light gray to dark black) representing PWM similarity (used in similarity-based methods). In (a), all of the TFs are from the same family (DMRT), and therefore have high levels of motif similarity (all the edges are dark). Our method is able to group them together because they co-occur often. In (b), the grouping has both intra- and extra-familial connections, with some TFs having dissimilar (light gray) PWMs. Many of these interactions could not be picked up a motif similarity-based method