PMID- 26647925
OWN - NLM
STAT- MEDLINE
DCOM- 20160927
LR  - 20181113
IS  - 1791-2423 (Electronic)
IS  - 1019-6439 (Print)
IS  - 1019-6439 (Linking)
VI  - 48
IP  - 2
DP  - 2016 Feb
TI  - Identifying molecular subtypes in human colon cancer using gene expression and 
      DNA methylation microarray data.
PG  - 690-702
LID - 10.3892/ijo.2015.3263 [doi]
AB  - 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.
FAU - Ren, Zhonglu
AU  - Ren Z
AD  - Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical 
      University, Guangzhou, Guangdong, P.R. China.
FAU - Wang, Wenhui
AU  - Wang W
AD  - Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical 
      University, Guangzhou, Guangdong, P.R. China.
FAU - Li, Jinming
AU  - Li J
AD  - Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical 
      University, Guangzhou, Guangdong, P.R. China.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20151124
PL  - Greece
TA  - Int J Oncol
JT  - International journal of oncology
JID - 9306042
RN  - 0 (Biomarkers, Tumor)
SB  - IM
MH  - Aged
MH  - Biomarkers, Tumor/genetics
MH  - Cluster Analysis
MH  - Colonic Neoplasms/*genetics
MH  - CpG Islands/genetics
MH  - DNA Methylation/*genetics
MH  - Female
MH  - Gene Expression/*genetics
MH  - Gene Expression Profiling/methods
MH  - Gene Expression Regulation, Neoplastic/*genetics
MH  - Genes, Neoplasm/genetics
MH  - Humans
MH  - Male
MH  - Oligonucleotide Array Sequence Analysis/methods
MH  - Phenotype
MH  - Up-Regulation/genetics
PMC - PMC4725456
EDAT- 2015/12/10 06:00
MHDA- 2016/09/28 06:00
PMCR- 2015/11/24
CRDT- 2015/12/10 06:00
PHST- 2015/10/10 00:00 [received]
PHST- 2015/11/11 00:00 [accepted]
PHST- 2015/12/10 06:00 [entrez]
PHST- 2015/12/10 06:00 [pubmed]
PHST- 2016/09/28 06:00 [medline]
PHST- 2015/11/24 00:00 [pmc-release]
AID - ijo-48-02-0690 [pii]
AID - 10.3892/ijo.2015.3263 [doi]
PST - ppublish
SO  - Int J Oncol. 2016 Feb;48(2):690-702. doi: 10.3892/ijo.2015.3263. Epub 2015 Nov 
      24.