Tissue Repair Subnetworks # RCR-capable nodes GSE18800 Bleomycin GSE5372 Mechanical Injury #consistent HYPs (%) #inconsistent HYPs (%) #consistent HYPs (%) #inconsistent HYPs (%) Cell Migration and Adhesion in Wound Healing 70 24 (34%) 5 (7%) 15 (21%) 2 (3%) Differentiation of Progenitor Cell in Wound Healing 12 1 (8%) 1 (8%) 2 (17%) 0 (0%) Fibrosis and EMT 97 43 (44%) 5 (5%) 24 (25%) 6 (6%) Immune Regulation of Tissue Repair 83 40 (48%) 5 (6%) 15 (18%) 4 (5%)

Table 3: Summary of results obtained with evaluation data sets. Shown are the numbers of RCR-capable nodes in each of the three subnetworks used for evaluation, as well as the number of HYPs matching these nodes that are predicted by RCR in the GSE18800 Bleomycin and GSE5372 Mechanical Injury data sets. HYPs may be predicted in directions either consistent or inconsistent with their regulation of the process in the subnetworks, relative to an increase in the process described by the subnetwork. Percentages are calculated based on the total number of RCR-capable nodes in each subnetwork.