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Distinguishing Rectal Cancer from Colon Cancer Based on the Support Vector Machine Method and RNA-sequencing Data

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Summary

Colorectal cancer (CRC) is the third most commonly diagnosed cancer worldwide. Several studies have indicated that rectal cancer is significantly different from colon cancer in terms of treatment, prognosis, and metastasis. Recently, the differential mRNA expression of colon cancer and rectal cancer has received a great deal of attention. The current study aimed to identify significant differences between colon cancer and rectal cancer based on RNA sequencing (RNA-seq) data via support vector machines (SVM). Here, 393 CRC samples from the The Cancer Genome Atlas (TCGA) database were investigated, including 298 patients with colon cancer and 95 with rectal cancer. Following the random forest (RF) analysis of the mRNA expression data, 96 genes such as HOXB13, PRAC, and BCLAF1 were identified and utilized to build the SVM classification model with the Leave-One-Out Cross-validation (LOOCV) algorithm. In the training (n=196) and the validation cohorts (n=197), the accuracy (82.1 % and 82.2 %, respectively) and the AUC (0.87 and 0.91, respectively) indicated that the established optimal SVM classification model distinguished colon cancer from rectal cancer reasonably. However, additional experiments are required to validate the predicted gene expression levels and functions.

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Author notes

  1. Both authors contributed equally to this work.

Authors and Affiliations

  1. Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, China

    Yan Zhang, Yuan Wu, Xiao-mei Zhang, Sheng Li, Yun Liu, Xin Guan & Bo Shen

  2. Shanghai Yunying Medical Technology Co., Ltd., Shanghai, 201612, China

    Zi-ying Gong, Hai-dan Ye, Xiao-kai Zhao, Jie-yi Li & Dao-yun Zhang

  3. Jiaxing Yunying Medical Inspection Co., Ltd., Jiaxing, 314000, China

    Zi-ying Gong, Hai-dan Ye, Xiao-kai Zhao, Jie-yi Li & Dao-yun Zhang

  4. School of Medicine, Jiangsu University, Zhenjiang, 212013, China

    Wei Zhu & Mei Wang

  5. School of Public Health, Southeast University, Nanjing, 211189, China

    Ge-yu Liang

Authors
  1. Yan Zhang
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  2. Yuan Wu
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Correspondence to Bo Shen.

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Conflict of Interest Statement

The authors declare that there is no conflict of interest with any financial organization or corporation or individual that can inappropriately influence this work.

This work was supported by the Six Talent Peaks Project in Jiangsu Province (No. 2014-wsw-017); Beijing Medical Award Foundation (No. YJHYXKYJJ-432); Foundation of Social Development Project of the Science and Technology Department of Jiangsu Province (No. BE2015719); Social Development Key Research and Development Plan of Jiangsu Province (No. BE2017694) and The Foundation of Nanjing Medical University (No. 2017NJMUZD140).

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Zhang, Y., Wu, Y., Gong, Zy. et al. Distinguishing Rectal Cancer from Colon Cancer Based on the Support Vector Machine Method and RNA-sequencing Data. CURR MED SCI 41, 368–374 (2021). https://doi.org/10.1007/s11596-021-2356-8

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  • DOI: https://doi.org/10.1007/s11596-021-2356-8

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