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Identifying molecular subtypes in human colon cancer using gene expression and DNA methylation microarray data

  • Authors:
    • Zhonglu Ren
    • Wenhui Wang
    • Jinming Li
  • View Affiliations / Copyright

    Affiliations: Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, P.R. China
    Copyright: © Ren et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Pages: 690-702
    |
    Published online on: November 24, 2015
       https://doi.org/10.3892/ijo.2015.3263
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Abstract

Identifying colon cancer subtypes based on molecular signatures may allow for a more rational, patient-specific approach to therapy in the future. Classifications using gene expression data have been attempted before with little concordance between the different studies carried out. In this study we aimed to uncover subtypes of colon cancer that have distinct biological characteristics and identify a set of novel biomarkers which could best reflect the clinical and/or biological characteristics of each subtype. Clustering analysis and discriminant analysis were utilized to discover the subtypes in two different molecular levels on 153 colon cancer samples from The Cancer Genome Atlas (TCGA) Data Portal. At gene expression level, we identified two major subtypes, ECL1 (expression cluster 1) and ECL2 (expression cluster 2) and a list of signature genes. Due to the heterogeneity of colon cancer, the subtype ECL1 can be further subdivided into three nested subclasses, and HOTAIR were found upregulated in subclass 2. At DNA methylation level, we uncovered three major subtypes, MCL1 (methylation cluster 1), MCL2 (methylation cluster 2) and MCL3 (methylation cluster 3). We found only three subtypes of CpG island methylator phenotype (CIMP) in colon cancer instead of the four subtypes in the previous reports, and we found no sufficient evidence to subdivide MCL3 into two distinct subgroups.
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Copy and paste a formatted citation
Spandidos Publications style
Ren Z, Wang W and Li J: Identifying molecular subtypes in human colon cancer using gene expression and DNA methylation microarray data. Int J Oncol 48: 690-702, 2016.
APA
Ren, Z., Wang, W., & Li, J. (2016). Identifying molecular subtypes in human colon cancer using gene expression and DNA methylation microarray data. International Journal of Oncology, 48, 690-702. https://doi.org/10.3892/ijo.2015.3263
MLA
Ren, Z., Wang, W., Li, J."Identifying molecular subtypes in human colon cancer using gene expression and DNA methylation microarray data". International Journal of Oncology 48.2 (2016): 690-702.
Chicago
Ren, Z., Wang, W., Li, J."Identifying molecular subtypes in human colon cancer using gene expression and DNA methylation microarray data". International Journal of Oncology 48, no. 2 (2016): 690-702. https://doi.org/10.3892/ijo.2015.3263
Copy and paste a formatted citation
x
Spandidos Publications style
Ren Z, Wang W and Li J: Identifying molecular subtypes in human colon cancer using gene expression and DNA methylation microarray data. Int J Oncol 48: 690-702, 2016.
APA
Ren, Z., Wang, W., & Li, J. (2016). Identifying molecular subtypes in human colon cancer using gene expression and DNA methylation microarray data. International Journal of Oncology, 48, 690-702. https://doi.org/10.3892/ijo.2015.3263
MLA
Ren, Z., Wang, W., Li, J."Identifying molecular subtypes in human colon cancer using gene expression and DNA methylation microarray data". International Journal of Oncology 48.2 (2016): 690-702.
Chicago
Ren, Z., Wang, W., Li, J."Identifying molecular subtypes in human colon cancer using gene expression and DNA methylation microarray data". International Journal of Oncology 48, no. 2 (2016): 690-702. https://doi.org/10.3892/ijo.2015.3263
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