Inferring gene regulatory networks using transcriptional profiles as dynamical attractors
Fig 6
(A) The schematic diagram of the S. cerevisiae synthetic circuit. Solid lines represent direct transcriptional regulation and dotted lines indicate indirect transcriptional regulation mediated by a protein-level activation or inhibition of a transcription factor. Edges accurately inferred by EA are labeled in green, otherwise in black. Gal80 protein can inhibit SWI5 transcription by preventing Gal4-mediated activation of target genes in the absence of galactose. Modified from the original paper [56]. (B) The schematic diagram of the inferred circuit. Additional inferred edges that are not present in the original design but are supported by previously published literature are labeled in orange. Inferred inhibitory edges indicated in red represent putative mechanisms for indirect repression of SWI5 by Gal80, but are not supported by known mechanisms of Gal80 function as discussed in the text.