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Inferring novel genes related to colorectal cancer via random walk with restart algorithm

Gene Therapy volume 26, pages 373–385 (2019)Cite this article

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Abstract

Colorectal cancer (CRC) is the third most common type of cancer. In recent decades, genomic analysis has played an increasingly important role in understanding the molecular mechanisms of CRC. However, its pathogenesis has not been fully uncovered. Identification of genes related to CRC as complete as possible is an important way to investigate its pathogenesis. Therefore, we proposed a new computational method for the identification of novel CRC-associated genes. The proposed method is based on existing proven CRC-associated genes, human protein–protein interaction networks, and random walk with restart algorithm. The utility of the method is indicated by comparing it to the methods based on Guilt-by-association or shortest path algorithm. Using the proposed method, we successfully identified 298 novel CRC-associated genes. Previous studies have validated the involvement of the majority of these 298 novel genes in CRC-associated biological processes, thus suggesting the efficacy and accuracy of our method.

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Acknowledgements

We would like to thank Dr. Yu-Hang Zhang from Shanghai Institutes for Biological Sciences for his useful advice.

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  1. Department of General Surgery, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute of Digestive Surgery, Shanghai, 200025, China

    Sheng Lu & Zheng-Gang Zhu

  2. Department of Chemistry, College of Sciences, Shanghai University, Shanghai, 200444, China

    Wen-Cong Lu

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  1. Sheng Lu
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  2. Zheng-Gang Zhu
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  3. Wen-Cong Lu
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Correspondence to Wen-Cong Lu.

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Lu, S., Zhu, ZG. & Lu, WC. Inferring novel genes related to colorectal cancer via random walk with restart algorithm. Gene Ther 26, 373–385 (2019). https://doi.org/10.1038/s41434-019-0090-7

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