Identifying Ulcerative Colitis- and Crohn’s Disease-Specific Subnets

Disease-specific PPI data for UC and CD were extracted using the PSICQUIC web service (October 29, 2020).² Then the KeyPathwayMiner (KPM)³ (version 5.0.1) plugin for Cytoscape was downloaded. The KPM plugin of Cytoscape is able to efficiently uncover all the maximum connected subnets in a biological network. The KPM algorithm processes transcriptome data, p-values as “1” or “0” (Alcaraz et al., 2016), so p-values are arranged as “1” for significantly expressed genes (SEGs) (with p-value < 0.05) and “0” for non-significantly expressed genes, respectively. The K-value, which is an important parameter for KPM, indicates how many nonsense genes will be in the module. The optimal K-value was determined as 5 by trial and error (Alcaraz et al., 2016), such that significant genes are missed when the K-value is below 5, and no new significant genes are added when above 5. In this study, after loading the disease-specific PPI networks to Cytoscape, genes and p-values obtained from {"type":"entrez-geo","attrs":{"text":"GSE126124","term_id":"126124"}}GSE126124 and {"type":"entrez-geo","attrs":{"text":"GSE3365","term_id":"3365"}}GSE3365 datasets were arranged in the appropriate format for KPM and uploaded as two separate files. The K-value was assumed to be 5; the transcriptome data in the two sets were logically connected using “AND” and mapped to the PPI network so that new modules for UC and CD were obtained.

The STRING database is designed to comprehensively combine, evaluate, and disseminate protein–protein relationship information (Franceschini et al., 2012). With StringApp⁴ (version 1.6.0), PPI queries can be performed in four different ways: protein query, PubMed query, disease query, and protein/compound query. In this study, the PPI network of DEGs in the two datasets was constructed using the STRING database, and an interaction with a composite score of > 0.95 was considered as statistically significant. Also, an interaction with a maximum protein count of 500 and a composite score of > 0.95 was considered statistically significant when querying the disease names (ulcerative colitis and Crohn’s disease) in the STRING database. In this way, DEG- and disease-specific PPI networks for UC and CD were merged (intersection analysis) with the Cytoscape application, and new intersection modules were obtained.