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)

本数据集包含以下内容：(1) 第二步中不同阈值下的富集比（补充图S1）；(2) 10个预测炎症基因的文献评价结果（补充表S1）；(3) 32个预测炎症调控因子的文献评价结果（补充表S2）；(4) 经由TSNBA完成的分子特征维基通路富集分析结果（补充表S3）；(5) 32个预测炎症调控因子的转录因子（Transcription Factor, TF）结合位点分析结果（补充表S4）；(6) 取自TFactS数据库的5种转录因子（即DLX5、MSX1、NR5A1、PRRX1及RXRA）所对应的转录因子-炎症基因关联关系（补充表S5）；(7) 经文献证实为炎症调控因子的9种转录因子的蛋白质相互作用数据（来自STRING数据库，补充表S6）；(8) 网络传播扩散参数α的相关研究结果（补充表S7）；(9) TSNBA第一步流程的方法对比结果（补充表S8）；(10) TSNBA的方法对比结果（补充表S9）；(11) 不同方法所得特征集合的并集文件（格式为XLSX）。