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The bioinformatics aspects of gene screening of HT-29, human colon cell line treated with caffeic acid

Majid Rezaei-Tavirani, Mostafa Rezaei-Tavirani, Mona Zamanian Azodi




Aim: To better understand the anticancer properties of coffee, bioinformatics analysis of gene expression profile of HT-29, human colon cell line in the exposure of caffeic acid (CA) is proposed in this study.

Background: Coffee as a popular beverage has been shown to be a potential health promoter as well as being effective on different kinds of diseases including cancer.

Methods: The differentially expressed genes (DEGs) across the comparison of groups of samples including none-treated HT-29 and HT-29 tread with CA were applied for the protein-protein interaction mapping. Cytoscape v.3.7.1 constructed a network and analyzed the topological features of the most noteworthy DEGs.

Results: The genes of CTSZ, AFF4, DHRS2, and HMGCS1 known as active agents in cancer progression, were identified as the central DEGs in the constructed PPI network in this study. Especially, HMGCS1 is the most central gene is also linked to one of the important colon cancer altered processes, cholesterol metabolism.

Conclusion: Lowering the risk of colon cancer could be perhaps through nominated DEGs and therefore, regulation of serum cholesterol as well as protection against cancer development.

Keywords: Coffee consumption, Colon cancer, Transcriptome, Protein-protein interaction network analysis, Biological process analysis.

(Please cite as: Rezaei-Tavirani M, Rezaei Tavirani M, Zamanian Azodi M. The bioinformatics aspects of gene screening of HT-29, human colon cell line treated with caffeic acid Gastroenterol Hepatol Bed Bench 2019;12(3):246-253).


Coffee consumption, Colon cancer, Transcriptome, Protein-protein interaction network analysis, Biological process analysis.


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DOI: https://doi.org/10.22037/ghfbb.v12i3.1620