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.
Schlitt and Brazma BMC Bioinformatics 2007 8(Suppl 6):S9 doi:10.1186/1471-2105-8-S6-S9