Assessment of colon cancer molecular mechanism: a system biology approach Assessment of colon cancer molecular mechanism: A System Biology Approach
Gastroenterology and Hepatology from Bed to Bench,
Vol. 14 No. Supplement 1 (2021),
30 December 2021
https://doi.org/10.22037/ghfbb.vi.2368
Abstract
Aim: The current study aimed to assess and compare colon cancer dysregulated genes from the GEO and STRING databases.
Background: Colorectal cancer is known as the third most common kind of cancer and the second most important reason for global cancer-related mortality rates. There have been many studies on the molecular mechanism of colon cancer
Methods: From the STRING database, 100 differentially expressed proteins related to colon cancers were retrieved and analyzed by network analysis. The central nodes of the network were assessed by gene ontology. The findings were compared with a GSE from GEO.
Results: Based on data from the STRING database, TP53, EGFR, HRAS, MYC, AKT1, GAPDH, KRAS, ERBB2, PTEN, and VEGFA were identified as central genes. The central nodes were not included in the significant DEGs of the analyzed GSE.
Conclusion: A combination of different database sources in system biology investigations provides useful information about the studied diseases.
Keywords:
- Colon cancer; Protein expression; Bioinformatics; Human; Network analysis
How to Cite
Arjmand , B. ., khodadost, M. ., Jahani Sherafat, S. ., Rezaei –Tavirani, M., Hamzeloo Moghadam, M., Rezaei Tavirani, S., Khanabadi, B., & Iranshahi, M. . (2021). Assessment of colon cancer molecular mechanism: a system biology approach: Assessment of colon cancer molecular mechanism: A System Biology Approach. Gastroenterology and Hepatology from Bed to Bench, 14(Supplement 1). https://doi.org/10.22037/ghfbb.vi.2368
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24. Freudlsperger C, Burnett JR, Friedman JA, Kannabiran VR, Chen Z, Van Waes C. EGFR–PI3K–AKT–mTOR signaling in head and neck squamous cell carcinomas: attractive targets for molecular-oriented therapy. Expert opinion on therapeutic targets. 2011;15(1):63-74.
25. Sun L, Zhang Q, Luan H, Zhan Z, Wang C, Sun B. Comparison of KRAS and EGFR gene status between primary non-small cell lung cancer and local lymph node metastases: implications for clinical practice. Journal of Experimental & Clinical Cancer Research. 2011;30(1):1-8.
26. Rostami-Nejad M, Razzaghi Z, Esmaeili S, Rezaei-Tavirani S, Baghban AA, Vafaee R. Immunological reactions by T cell and regulation of crucial genes in treated celiac disease patients. Gastroenterology and hepatology from bed to bench. 2020;13(2):155.
27. Rezaei-Tavirani M, Nejad MR, Arjmand B, Tavirani SR, Razzaghi M, Mansouri V. Fibrinogen Dysregulation is a Prominent Process in Fatal Conditions of COVID-19 Infection; a Proteomic Analysis. Archives of Academic Emergency Medicine. 2021;9(1):e26-e.
2. Feng H-T, Zou S, Chen M, Xiong F, Lee M-H, Fang L, et al. Tuning push–pull electronic effects of AIEgens to boost the theranostic efficacy for colon cancer. Journal of the American Chemical Society. 2020;142(26):11442-50.
3. Long J, Guan P, Hu X, Yang L, He L, Lin Q, et al. Natural polyphenols as targeted modulators in colon cancer: Molecular mechanisms and Applications. Frontiers in Immunology. 2021;12.
4. Folkesson E, Niederdorfer B, Nakstad VT, Thommesen L, Klinkenberg G, Lægreid A, et al. High-throughput screening reveals higher synergistic effect of MEK inhibitor combinations in colon cancer spheroids. Scientific reports. 2020;10(1):1-14.
5. Ostrowski J, Wyrwicz LS. Integrating genomics, proteomics and bioinformatics in translational studies of molecular medicine. Expert review of molecular diagnostics. 2009;9(6):623-30.
6. Tang H, Mirshahidi S, Senthil M, Kazanjian K, Chen C-S, Zhang K. Down-regulation of LXR/RXR activation and negative acute phase response pathways in colon adenocarcinoma revealed by proteomics and bioinformatics analysis. Cancer Biomarkers. 2014;14(5):313-24.
7. Peng Q, Lin K, Chang T, Zou L, Xing P, Shen Y, et al. Identification of genomic expression differences between right-sided and left-sided colon cancer based on bioinformatics analysis. OncoTargets and therapy. 2018;11:609.
8. Yang H, Wu J, Zhang J, Yang Z, Jin W, Li Y, et al. Integrated bioinformatics analysis of key genes involved in progress of colon cancer. Molecular genetics & genomic medicine. 2019;7(4):e00588.
9. Wang Z, Cui B, Zhang F, Yang Y, Shen X, Li Z, et al. Development of a correlative strategy to discover colorectal tumor tissue derived metabolite biomarkers in plasma using untargeted metabolomics. Analytical chemistry. 2018;91(3):2401-8.
10. Schumacher Y, Aparicio T, Ourabah S, Baraille F, Martin A, Wind P, et al. Dysregulated CRTC1 activity is a novel component of PGE2 signaling that contributes to colon cancer growth. Oncogene. 2016;35(20):2602-14.
11. Wang Y, Xue D, Li Y, Pan X, Zhang X, Kuang B, et al. The long noncoding RNA MALAT-1 is a novel biomarker in various cancers: a meta-analysis based on the GEO database and literature. Journal of Cancer. 2016;7(8):991.
12. Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau W-C, Ledoux P, et al. NCBI GEO: mining millions of expression profiles—database and tools. Nucleic acids research. 2005;33(suppl_1):D562-D6.
13. Clough E, Barrett T. The gene expression omnibus database. Statistical genomics: Springer; 2016. p. 93-110.
14. Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, et al. The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible. Nucleic acids research. 2016:gkw937.
15. Doncheva NT, Morris JH, Gorodkin J, Jensen LJ. Cytoscape StringApp: network analysis and visualization of proteomics data. Journal of proteome research. 2018;18(2):623-32.
16. Asadzadeh-Aghdaei H, Okhovatian F, Razzaghi Z, Heidari M, Vafaee R, Nikzamir A. Radiation Therapy in Patients With Brain Cancer: Post-proteomics Interpretation. Journal of lasers in medical sciences. 2019;10(Suppl 1):S59.
17. Azodi MZ, Arjmand B, Zali A, Razzaghi M. Introducing APOA1 as a key protein in COVID-19 infection: a bioinformatics approach. Gastroenterology and hepatology from bed to bench. 2020;13(4):367.
18. Azodi MZ, Rezaei-Tavirani M, Nejad MR, Rezaei-Tavirani M. Human prolactinoma: A view of protein-protein interaction pattern. International journal of endocrinology and metabolism. 2018;16(4).
19. Azodi MZ, Arjmand B, Razzaghi M, Tavirani MR, Ahmadzadeh A, Rostaminejad M. Platelet and Haemostasis are the Main Targets in Severe Cases of COVID-19 Infection; a System Bioinformatics Study. Archives of Academic Emergency Medicine. 2021;9(1):e27-e.
20. Hsing M, Byler KG, Cherkasov A. The use of Gene Ontology terms for predicting highly-connected'hub'nodes in protein-protein interaction networks. BMC systems biology. 2008;2(1):1-14.
21. Olivier M, Hollstein M, Hainaut P. TP53 mutations in human cancers: origins, consequences, and clinical use. Cold Spring Harbor perspectives in biology. 2010;2(1):a001008.
22. McLoughlin N, Yin D, Maltby L, Wood RM, Yu H. Evaluation of sensitivity and specificity of two crustacean biochemical biomarkers. Environmental Toxicology and Chemistry: An International Journal. 2000;19(8):2085-92.
23. Mansouri V, Tavirani MR, Tavirani SR. Gene screening of colorectal cancers via network analysis. Gastroenterology and hepatology from bed to bench. 2019;12(2):149.
24. Freudlsperger C, Burnett JR, Friedman JA, Kannabiran VR, Chen Z, Van Waes C. EGFR–PI3K–AKT–mTOR signaling in head and neck squamous cell carcinomas: attractive targets for molecular-oriented therapy. Expert opinion on therapeutic targets. 2011;15(1):63-74.
25. Sun L, Zhang Q, Luan H, Zhan Z, Wang C, Sun B. Comparison of KRAS and EGFR gene status between primary non-small cell lung cancer and local lymph node metastases: implications for clinical practice. Journal of Experimental & Clinical Cancer Research. 2011;30(1):1-8.
26. Rostami-Nejad M, Razzaghi Z, Esmaeili S, Rezaei-Tavirani S, Baghban AA, Vafaee R. Immunological reactions by T cell and regulation of crucial genes in treated celiac disease patients. Gastroenterology and hepatology from bed to bench. 2020;13(2):155.
27. Rezaei-Tavirani M, Nejad MR, Arjmand B, Tavirani SR, Razzaghi M, Mansouri V. Fibrinogen Dysregulation is a Prominent Process in Fatal Conditions of COVID-19 Infection; a Proteomic Analysis. Archives of Academic Emergency Medicine. 2021;9(1):e26-e.
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