Fig. 1.

Overview of the ALPHABIT pipeline. (A) In a model of cooperativity, the binding of one factor depends on the binding of another. For example, when a STAT1 motif is present, both STAT1 and NFκB are bound. Loss of the STAT1 motif decreases binding of NFκB, despite the presence of an NFκB motif. (B) Associated factor discovery process. Variable motifs are searched for in variable NFκB binding peaks and the difference in “motif score” (i.e., match to consensus) is correlated with difference in NFκB binding. Significant predictions are validated by ChIP-Seq and subject to subsequent analysis.