File S1 - A Three Step Network Based Approach (TSNBA) to Finding Disease Molecular Signature and Key Regulators: A Case Study of IL-1 and TNF-Alpha Stimulated Inflammation

Including the following: (1) Enrichment ratios under different thresholds in the second step (Figure S1); (2) literature evaluation for 10 predicted inflammatory genes (Table S1); (3) literature evaluation for 32 predicted regulators of inflammation (Table S2); (4) wikipathway enrichment analysis of molecular signatures via TSNBA (Table S3); (5) TF binding sites analysis of 32 predicted regulators of inflammation (Table S4); (6) transcription factor-inflammatory gene relationships from TFactS for 5 transcription factors, namely DLX5, MSX1, NR5A1, PRRX1, and RXRA (Table S5); (7) protein-protein interactions collected from STRING database for 9 transcription factors that are confirmed by literature to be inflammatory regulators (Table S6); (8) investigation for diffusion parameter α of network propagation (Table S7); (9) methods comparison for the first step of TSNBA (Table S8); (10) methods comparison for TSNBA (Table S9); (11) union sets of signatures from different methods. (XLSX)