ArticleInternational journal of oncology2016
Identifying molecular subtypes in human colon cancer using gene expression and DNA methylation microarray data.
Article in International journal of oncology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
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Who cites it
15 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Aberrant methylation patterns in colorectal cancer: a meta-analysis.Oncotarget · 2017Pooled it
- The Different Immune Response Between Onset and Remission of AQP4 Antibody-Positive Optic Neuritis Based on RNA Sequencing of Whole Blood.Journal of inflammation research · 2025Article
- Omada: robust clustering of transcriptomes through multiple testing.GigaScience · 2024Article
- In Silico Gene Prioritization Highlights the Significance of Bone Morphogenetic Protein 4 (International journal of molecular sciences · 2023Article
- Comparison of Methods for Feature Selection in Clustering of High-Dimensional RNA-Sequencing Data to Identify Cancer Subtypes.Frontiers in genetics · 2021Article
- Analysis of 5-Methylcytosine Regulators and DNA Methylation-Driven Genes in Colon Cancer.Frontiers in cell and developmental biology · 2021Article
- Identification of Distinct Molecular Patterns and a Four-Gene Signature in Colon Cancer Based on Invasion-Related Genes.Frontiers in genetics · 2021Article
- Methylome and transcriptome analyses reveal insights into the epigenetic basis for the good survival of hypomethylated ER-positive breast cancer subtype.Clinical epigenetics · 2020Article
- Stratification of Breast Cancer by Integrating Gene Expression Data and Clinical Variables.Molecules (Basel, Switzerland) · 2019Article
- Cluster analysis on high dimensional RNA-seq data with applications to cancer research - An evaluation study.PloS one · 2019Article
- Identification of key differentially expressed MicroRNAs in cancer patients through pan-cancer analysis.Computers in biology and medicine · 2018Article
- LncRNA UCA1, Upregulated in CRC Biopsies and Downregulated in Serum Exosomes, Controls mRNA Expression by RNA-RNA Interactions.Molecular therapy. Nucleic acids · 2018Article
- An Integrated Approach for Identifying Molecular Subtypes in Human Colon Cancer Using Gene Expression Data.Genes · 2018Article
- Robust Significance Analysis of Microarrays by MinimumBioMed research international · 2017Article
- Multiplexed Liquid Chromatography-Multiple Reaction Monitoring Mass Spectrometry Quantification of Cancer Signaling Proteins.Methods in molecular biology (Clifton, N.J.) · 2017Article
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3 authors.
Funding
No grant is acknowledged in the PubMed record.
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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