Additional file 3 of The Local Edge Machine: inference of dynamic models of gene regulation

Table: Evidence for regulatory interactions in yeast cell-cycle networks 1–5. Each row corresponds to a regulatory interaction (edge), where an upstream regulator acts on a target gene. p values from four high-throughput chromatin immunoprecipitation (ChIP) studies are shown to provide evidence (when available) for a regulator transcription factor (TF) binding to a target promoter [11, 50, 51]. ChIP p values were combined using Fisher’s method [52]. Combined p values less than 0.001 were considered high-confidence evidence for a given edge (shown in bold red). Where available, edges are supported by additional literature references (see Additional file 8). In the absence of ChIP data, literature evidence was used to determine edges. Evidence for many edges provided here is also documented in the YEASTRACT database [42]. The direction of each interaction (activation, repression, or N/A unknown) is derived from the YEASTRACT database, literature evidence, and/or biological priors about gene function (see Additional file 1). (XLSX 75 kb)