Additional file 17 of The Local Edge Machine: inference of dynamic models of gene regulation

Table: Ranking of candidate circadian regulators. We used LEM to discover new potential regulators of circadian core nodes (see Additional file 16) by first selecting the top periodic gene sets from 12 mouse organs (see Additional file 1: Section 12) and then using LEM to identify genes that appear likely to regulate core elements in multiple organs. We obtained a final list of 354 candidate genes (333 top potential regulators plus the 21 core nodes that do appear in the set of 333), of which 205 were either in the set of 31 known core genes or passed the JTK_CYCLE periodicity cutoff of 0.1 for the mouse liver dataset. This table lists the 205 gene common names (column 1), mouse genome database IDs (column 6), and microarray probe IDs (column 5). Additionally, the table marks core nodes with an â xâ (column 7) and provides the JTK_CYCLE periodicity p value (column 11). Next, we ran full LEM with 205 nodes using mouse liver data. For each of the 205 candidates, we extracted the maximum LEM probability score for any core element targeting each candidate (column 2) and the maximum score for each candidate regulating any core node (column 3). The candidate list is ranked by the product of these two probabilities (column 4). Finally, we compared our candidate list to a compilation of genes with known circadian function (column 7), reviewed by Zhang et al. [12]. (TXT 20 kb)