Identifying miRNA and gene modules of colon cancer associated with pathological stage by weighted gene co-expression network analysis

OncoTargets and Therapy
Xian-Guo ZhouQiu-Yan Wang

Abstract

Colorectal cancer (CRC) is the fourth most common cause of cancer-related mortality worldwide. The tumor, node, metastasis (TNM) stage remains the standard for CRC prognostication. Identification of meaningful microRNA (miRNA) and gene modules or representative biomarkers related to the pathological stage of colon cancer helps to predict prognosis and reveal the mechanisms behind cancer progression. We applied a systems biology approach by combining differential expression analysis and weighted gene co-expression network analysis (WGCNA) to detect the pathological stage-related miRNA and gene modules and construct a miRNA-gene network. The Cancer Genome Atlas (TCGA) colon adenocarcinoma (CAC) RNA-sequencing data and miRNA-sequencing data were subjected to WGCNA analysis, and the GSE29623, GSE35602 and GSE39396 were utilized to validate and characterize the results of WGCNA. Two gene modules (Gmagenta and Ggreen) and one miRNA module were associated with the pathological stage. Six hub genes (COL1A2, THBS2, BGN, COL1A1, TAGLN and DACT3) were related to prognosis and validated to be associated with the pathological stage. Five hub miRNAs were identified to be related to prognosis (hsa-miR-125b-5p, hsa-miR-145-5p, hsa-let-7c-5p, h...Continue Reading

Citations

Feb 19, 2019·Journal of Cellular Biochemistry·Baojin XuJie Lin
Jan 16, 2020·The Journal of International Medical Research·Jungang LiuWeizhong Tang
Jun 22, 2019·Journal of Translational Medicine·Berta Roman-CanalEva Colas
Jun 27, 2020·Nutrition and Cancer·Xiaolin HouMinghui Pang
Apr 28, 2020·BioMed Research International·Kaisheng LiuXiao Wang
Jul 25, 2020·Scientific Reports·Rafael Parra-MedinaCésar Payán-Gómez
Dec 20, 2018·Journal of Cellular Biochemistry·Xiaojie WangPan Chi
Jan 29, 2019·Cancer Biomarkers : Section a of Disease Markers·Shengjun Shi, Binqun Tian
May 9, 2019·United European Gastroenterology Journal·Longchang HuangTong Wang
Mar 27, 2020·Frontiers in Bioengineering and Biotechnology·Junfeng ZhuQi Zhao
Feb 7, 2020·Inflammation Research : Official Journal of the European Histamine Research Society ... [et Al.]·Jiamin HuangBingwei Sun
Feb 9, 2019·Digestive Diseases and Sciences·Jingwei LiuChengzhong Xing
Dec 22, 2020·Cancer Control : Journal of the Moffitt Cancer Center·Nanzheng ChenQifei Wu
Dec 19, 2020·Molecular Therapy. Nucleic Acids·Liaoran NiuDaiming Fan
Feb 11, 2021·The Journal of Physical Chemistry. B·Klára SchulcBorbála M Kovács
Jan 9, 2021·Journal of Translational Medicine·Jungang LiuWeizhong Tang
Feb 6, 2021·Environmental Toxicology and Pharmacology·Ying CaiXinyun Xu
Mar 14, 2021·NPJ Systems Biology and Applications·Sara PidòMarco Masseroli
Apr 11, 2021·Clinical and Experimental Medicine·Daye Yang, Dewei Zhang

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Datasets Mentioned

BETA
GSE28364
GSE39582
GSE29621
GSE29622
GSE29623

Methods Mentioned

BETA
sequence-based predictions
fluorescence-activated cell sorting

Software Mentioned

Gmagenta
DIANA
MCODE
Cytoscape
Mblack
microT
edgeR
Molecular Complex Detection ( MCODE )
R
WGCNA

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