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Identification of Key Genes Associated with Colorectal Cancer Based on the Transcriptional Network

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Pathology & Oncology Research

Abstract

Colorectal cancer (CRC) is among the most lethal human cancers, but the mechanism of the cancer is still unclear enough. We aimed to explore the key genes in CRC progression. The gene expression profile (GSE4183) of CRC was obtained from Gene Expression Omnibus database which included 8 normal samples, 15 adenoma samples, 15 CRC samples and 15 inflammatory bowel disease (IBD) samples. Thereinto, 8 normal, 15 adenoma, and 15 CRC samples were chosen for our research. The differentially expressed genes (DEGs) in normal vs. adenoma, normal vs. CRC, and adenoma vs. CRC, were identified using the Wilcoxon test method in R respectively. The interactive network of DEGs was constructed to select the significant modules using the Pearson’s correlation. Meanwhile, transcriptional network of DEGs was also constructed using the g: Profiler. Totally, 2,741 DEGs in normal vs. adenoma, 1,484 DEGs in normal vs. CRC, and 396 DEGs in adenoma vs. CRC were identified. Moreover, function analysis of DEGs in each group showed FcR-mediated phagocytosis pathway in module 1, cardiac muscle contraction pathway in module 6, and Jak-STAT signaling pathway in module 19 were also enriched. Furthermore, MZF1 and AP2 were the transcription factor in module 6, with the target SP1, while SP1 was also a transcription in module 20. DEGs like NCF1, AKT, SP1, AP2, MZF1, and TPM might be used as specific biomarkers in CRC development. Therapy targeting on the functions of these key genes might provide novel perspective for CRC treatment.

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Acknowledgments

This study was supported by Shanghai medical key subject construction project (NO.ZK2012A28), Key National Clinical Discipline construction project (2013)

Conflict of Interest

The Authors declare that they have no conflicts of interest to disclose.

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Authors and Affiliations

  1. Department of Emergency Surgery, East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai, 200120, China

    Guoting Chen, Xianping Niu, Guofeng Li, Ning Han, Xin Li, Guang Li, Yangzhou Liu, Guixin Sun, Yong Wang, Zengchun Li & Qinchuan Li

  2. Department of General Surgery, Shandong Laigang Hoaspital, Laiwu, Shandong Province, 271126, China

    Hengping Li

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  1. Guoting Chen
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  2. Hengping Li
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  3. Xianping Niu
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  4. Guofeng Li
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  5. Ning Han
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  6. Xin Li
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  7. Guang Li
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  9. Guixin Sun
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  10. Yong Wang
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  11. Zengchun Li
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  12. Qinchuan Li
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Corresponding author

Correspondence to Qinchuan Li.

Additional information

Guoting Chen and Hengping Li contributed equally to this work.

Highlights:

1. NCF1 might be a biomarker for colon adenoma.

2. AKT and TPM contribute to the CRC development.

3. MZF1 might act as a promoter in CRC progression.

4. SP1, regulated by AP2, might prevent the CRC progression.

5. Three significant pathways related to CRC were enriched.

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Chen, G., Li, H., Niu, X. et al. Identification of Key Genes Associated with Colorectal Cancer Based on the Transcriptional Network. Pathol. Oncol. Res. 21, 719–725 (2015). https://doi.org/10.1007/s12253-014-9880-9

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  • DOI: https://doi.org/10.1007/s12253-014-9880-9

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