Network Building Data Sets Network Evaluation Data Sets Process Bleomycin Hypoxia Bleomycin Mechanical Injury Data Set ID GSE25640 GSE11341 GSE18800 GSE5372 Pub Med ID 21602491 18469115 19966781 17164391 Species Mouse Human Mouse Human Context In vivo In vitro In vivo In vivo Cell Type Whole Lung Lung Endothelial cells Whole lung Airway epithelium from non-smokers Insult Bleomycin 7.5 U/kg Hypoxia 1% O2 Bleomycin 1 mg/kg Brushing to denude epithelium Timepoint(s) 21 days post treatment 48 hours 14 days post treatment 7 days post treatment Control Saline Day 21 Normoxia 21% O2 Saline Day 0 Day 0 Measured Endpoint Hydroxyproline, BAL inflammatory cells, Lung T-cells GREM1 protein, CXCR7 gene expression Hydroxyproline, at Day 21; TGFβ1 and BAL inflammatory cells at Day 7 and 21 Partially differentiated epithelial layer, <1% of sample is inflammatory cells # State Changes 2672 639 3425 1101 # of HYPs 501 292 521 265

Table 1: Data sets analyzed by RCR for network augmentation and evaluation.