Dataset Information

Identification of hub genes and outcome in colon cancer based on bioinformatics analysis.

ABSTRACT:

Background

Colon cancer is one of the leading malignant neoplasms worldwide. Until now, the concrete mechanisms of colonic cancerogenesis are largely unknown; identification of driven genes and pathways is, therefore, of great importance for monitoring and conquering this disease. This study aims to explore the potential biomarkers and therapeutic targets for colon cancer treatment.

Methods

The gene expression profile of GSE44076 from Gene Expression Omnibus database, including 98 primary colon cancers and 98 normal distant colon mucosa, was deeply analyzed. GEO2R tool was used to screen the differentially expressed genes (DEGs) between colon cancer tissues and normal samples. Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis were performed for screening DEGs using Database for Annotation, Visualization and Integrated Discovery database and Panther database. Moreover, Search Tool for the Retrieval of Interacting Genes, Cytoscape software, and Molecular Complex Detection plug-in were used to visualize the protein-protein interaction of these DEGs.

Results

A total of 497 DEGs were obtained, including 129 upregulated genes mainly enriched in Hippo signaling pathway, Wnt signaling pathway, and cytokine-cytokine receptor interaction and 368 downregulated genes enriched in retinol metabolism, steroid hormone biosynthesis, drug metabolism, and chemical carcinogenesis. Using Molecular Complex Detection software, three important modules were selected from the protein-protein interaction network. Moreover, 20 hub genes with high degree of connectivity were selected, including COL1A1, CXCL5, GNG4, TIMP1, and so on. The Kaplan-Meier analysis for overall survival and correlation analysis were applied among the hub genes.

Conclusion

Taken together, DEGs, especially the hub genes such as COL1A1, might be the driven genes in colon cancer progression. More importantly, they might be the novel biomarkers for diagnosis and guiding therapeutic strategies of colon cancer.

SUBMITTER: Yang W

PROVIDER: S-EPMC6312054 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Publications

Identification of hub genes and outcome in colon cancer based on bioinformatics analysis.

Yang Wanli W Ma Jiaojiao J Zhou Wei W Li Zichao Z Zhou Xin X Cao Bo B Zhang Yujie Y Liu Jinqiang J Yang Zhiping Z Zhang Hongwei H Zhao Qingchuan Q Hong Liu L Fan Daiming D

Cancer management and research 20181227

<h4>Background</h4>Colon cancer is one of the leading malignant neoplasms worldwide. Until now, the concrete mechanisms of colonic cancerogenesis are largely unknown; identification of driven genes and pathways is, therefore, of great importance for monitoring and conquering this disease. This study aims to explore the potential biomarkers and therapeutic targets for colon cancer treatment.<h4>Methods</h4>The gene expression profile of GSE44076 from Gene Expression Omnibus database, including 98 ...[more]

PMID: 30643458

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Dataset Information

Identification of hub genes and outcome in colon cancer based on bioinformatics analysis.

Background

Methods

Results

Conclusion

Publications

Identification of hub genes and outcome in colon cancer based on bioinformatics analysis.

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