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 1â 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 Fisherâ 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)

表：酵母细胞周期网络调控互作证据（1~5）。每一行代表一条调控互作（边），描述上游调控因子对靶基因的调控作用。四项高通量染色质免疫沉淀（chromatin immunoprecipitation, ChIP）研究得到的p值，可用于佐证调控转录因子（transcription factor, TF）结合靶基因启动子的情况（若存在对应数据）[11, 50, 51]。采用费舍尔（Fisher）合并法[52]对ChIP实验得到的p值进行合并。合并后的p值小于0.001时，即视为对应调控边的高可信度证据，此类证据以加粗红色标注。若有可用数据，调控边还可通过额外的文献参考文献进行佐证（详见补充文件8）。若无ChIP实验数据，则通过文献证据确定调控边。本文提供的多数调控边证据已在YEASTRACT数据库[42]中完成归档。每条调控互作的方向（激活、抑制或N/A，代表未知）均来源于YEASTRACT数据库、文献证据及/或基因功能相关的生物学先验知识（详见补充文件1）。（XLSX 75 kb）