Materials and Methods - Kur1sutaru/system_biology_mps GitHub Wiki

Gene Expression Omnibus (GEO - Edgar et al., 2002; Barret et al., 2013) - GSE111906, GSE95224, GSE23075, GSE15758, and GSE76283.
String - Without text mining. No first and second shell selection. String v.11.0 (Szklarczyk et al., 2019). *** Cytoscape**: MCODE v.1.6.1 (Bader & Hogue, 2003), Cytohubba v.0.1 (Chin et al., 2014), Centiscape v.2.2 (Scardoni et al., 2014), BiNGO v.3.0.4 (Maere et al., 2005, and CluePedia v.2.5.7 (Bindea et al., 2009; Bindea et al., 2013).
Statistical analysis - The functional enrichment was quantitatively assessed (p-value) using a hypergeometric distribution. Multiple test correction was also implemented by applying the false discovery rate (FDR) algorithm (Benjamini and Hochberg 1995) at a significance level of p < 0.05.