Direct and indirect effects. Red arcs are from the mutant network, green arcs from the ChIP network. A In the mutant where transcription factor A is deleted (disrupted) the expression of gene B is significantly different from its expression in the wild type. The transcription factor A does not bind to the putative promoter region of gene B (no green arc), but to the putative promoter region of transcription factor C, which in turn is found in the putative promoter region of gene B. This indirect path from A to B in the ChIP network might therefore explain the direct path in the mutant network. B All direct effects in the mutant network that could be explained by indirect paths via one additional transcription factor in the ChIP network.