In Silico Identification of Hub Genes as Observing Biomarkers for Gastric Cancer Metastasis

Author:

Ajucarmelprecilla Arulprakasam1ORCID,Pandi Jhansi12ORCID,Dhandapani Ranjithkumar3ORCID,Ramanathan Saikishore1ORCID,Chinnappan Jayaprakash3ORCID,Paramasivam Ragul2ORCID,Thangavelu Sathiamoorthi1ORCID,Mohammed Ghilan Abdul-Kareem4,Aljohani Saad Ali S.5,Oyouni Atif Abdulwahab A.67ORCID,Farasani Abdullah89ORCID,Altayar Malik A.10ORCID,Althagafi Hussam Awwadh E.11ORCID,Alzahrani Othman R.67,Durairaj Kaliannan12ORCID,Shrestha Anupama1314ORCID

Affiliation:

1. Medical Microbiology Unit, Department of Microbiology, Alagappa University, Karaikudi, Tamil Nadu, India

2. Chimertech Private Limited, Chennai, India

3. Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India

4. Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia

5. Department of Basic Medical Sciences, Faculty of Medicine, Alrayan Colleges, Almadinah Almunawarah, Saudi Arabia

6. Department of Biology, Faculty of Sciences, University of Tabuk, Tabuk, Saudi Arabia

7. Genome and Biotechnology Unit, Faculty of Sciences, University of Tabuk, Tabuk, Saudi Arabia

8. Biomedical Research Unit, Medical Research Center, Jazan University, Jazan 45142, Saudi Arabia

9. Department of Medical Laboratory Technology, College of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia

10. Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia

11. Biology Department, Faculty of Science and Arts, Al-Mikhwah, Al-Baha University, Saudi Arabia

12. Zoonosis Research Center, School of Medicine, Wonkwang University, Iksan, Republic of Korea

13. Research Institute of Agriculture and Applied Science, Tokha Kathmandu 2356, Nepal

14. Department of Plant Protection, Himalayan College of Agricultural Sciences and Technology, Kalanki, 44600 Kathmandu, Nepal

Abstract

Perception of hub genes engaged in metastatic gastric cancer (mGC) promotes novel ways to diagnose and treat the illness. The goal of this investigation is to recognize the hub genes and reveal its molecular mechanism. In order to explore the potential facts for gastric cancer, the expression profiles of two different datasets were used (GSE161533 and GSE54129). The genes were confirmed to be part of the PPI network for gastric cancer pathogenesis and prognosis. In Cytoscape, the CytoHubba module was used to discover the hub genes. Responsible hub genes were identified. Data from Kaplan–Meier plotter confirmed the predictive value of these distinct genes in various stages of gastric malignancy. Upregulated and downregulated genes were identified to utilize for further analysis. Positive regulation by a host of viral process, positive regulation of granulocyte differentiation, negative regulation of histone H3–K9 methylation were found in DEGs analysis. In addition, five KEGG pathways were identified as an essential enhancer that include nucleotide excision repair; base excision repair; DNA replication; homologous recombination; and complement and coagulation cascades. POLE, BUB1B, POLD4, C3, BLM, CCT7, PRPF31, APEX1, PSMA7, and CDC45 were chosen as hub genes after combining the PPI results. Our study recommends that BUB1B, CCT7, APEX1, PSMA7, and CDC45 might be potential biomarkers for gastric cancer. These biomarkers are upregulated genes. Therefore, suppression of these genes will increase the survival rate in gastric cancer patients.

Funder

Bharathiar University

Publisher

Hindawi Limited

Subject

Complementary and alternative medicine

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