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  • Title: Identification of potential crucial genes and key pathways shared in Inflammatory Bowel Disease and cervical cancer by machine learning and integrated bioinformatics.
    Author: Nguyen TB, Do DN, Nguyen-Thi ML, Hoang-The H, Tran TT, Nguyen-Thanh T.
    Journal: Comput Biol Med; 2022 Oct; 149():105996. PubMed ID: 36049413.
    Abstract:
    BACKGROUND: Recently, Inflammatory Bowel Disease (IBD) has been proven as a risk factor for the increasing incidence of cervical cancer (CC) development. In this study, we identify these potential hub genes and their significant pathways that commonly interact between IBD and CC and these pathological mechanisms. To this end, we use bioinformatics and systems biology approaches to analyze the miRNA-mRNA, TFs-mRNA regulatory network. METHODS AND FINDINGS: The reanalysis dataset from Gene Expression Omnibus (GEO) and the cancer genome atlas (TCGA) found these common differentially expressed genes (DEGs) between IBD and CC, clustered via weighted gene co-expression network analysis, and the vital modules significantly related to cervical cancer were identified. These hub genes of the key module were identified and explored in biological mechanism pathway analysis. Organelle fission, nuclear envelope, protein serine/threonine kinase activity, and the Human T-cell leukemia virus 1 infection pathway were the major enriched pathways for the common DEGs. Due to the high connectivity, the common DEGs with protein-protein interaction (PPI) network disclosed hub proteins (CDK1, MAD2L1, and CCNB1). This study also showed the classification algorithms of ten hub genes (MAD2L1, CCNB2, CDK1, CCNA2, BUB1B, KIF11, TTK, BUB1, CCNB1, ASPM) with accuracy >0.90 suggesting the novel biomarker potential of the hub genes. The microRNAs (miRNA), and transcription factors (TFs) mRNA regulatory network, five transcription factors, and twelve miRNAs are strongly linked to three hub genes. Gene drug interaction analysis found seven drugs compound that interacts with the hub gene. CONCLUSIONS: In the current study, our procedure has hypothesized the comprehensive understanding of disease mechanisms vital for both CC and IBD that may mediate their interaction. Our results suggest the further investigation of the molecules for the treatment of IBD and CC.
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