scholarly journals Gene Coexpression Network Alignment and Conservation of Gene Modules between Two Grass Species: Maize and Rice

2011 ◽  
Vol 156 (3) ◽  
pp. 1244-1256 ◽  
Author(s):  
Stephen P. Ficklin ◽  
F. Alex Feltus
Keyword(s):  
Network Alignment ◽  
Coexpression Network ◽  
Grass Species ◽  
Gene Coexpression Network ◽  
Gene Coexpression ◽  
Gene Modules

scholarly journals Weighted Gene Coexpression Network Analysis Reveals the Dynamic Transcriptome Regulation and Prognostic Biomarkers of Hepatocellular Carcinoma

2020 ◽  
Vol 16 ◽  
pp. 117693432092056
Author(s):  
Shuping Qu ◽  
Qiuyuan Shi ◽  
Jing Xu ◽  
Wanwan Yi ◽  
Hengwei Fan
Keyword(s):  
Hepatocellular Carcinoma ◽  
Differentially Expressed ◽  
Prognostic Biomarkers ◽  
Coexpression Network ◽  
Data Sets ◽  
Independent Data ◽  
Gene Coexpression Network ◽  
Gene Coexpression ◽  
Gene Modules ◽  
Coexpression Network Analysis

This study was aimed at revealing the dynamic regulation of mRNAs, long noncoding RNAs (lncRNAs), and microRNAs (miRNAs) in hepatocellular carcinoma (HCC) and to identify HCC biomarkers capable of predicting prognosis. Differentially expressed mRNAs (DEmRNAs), lncRNAs, and miRNAs were acquired by comparing expression profiles of HCC with normal samples, using an expression data set from The Cancer Genome Atlas. Altered biological functions and pathways in HCC were analyzed by subjecting DEmRNAs to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis. Gene modules significantly associated with disease status were identified by weighted gene coexpression network analysis. An lncRNA-mRNA and an miRNA-mRNA coexpression network were constructed for genes in disease-related modules, followed by the identification of prognostic biomarkers using Kaplan-Meier survival analysis. Differential expression and association with the prognosis of 4 miRNAs were verified in independent data sets. A total of 1220 differentially expressed genes were identified between HCC and normal samples. Differentially expressed mRNAs were significantly enriched in functions and pathways related to “plasma membrane structure,” “sensory perception,” “metabolism,” and “cell proliferation.” Two disease-associated gene modules were identified. Among genes in lncRNA-mRNA and miRNA-mRNA coexpression networks, 9 DEmRNAs and 7 DEmiRNAs were identified to be potential prognostic biomarkers. MIMAT0000102, MIMAT0003882, and MIMAT0004677 were successfully validated in independent data sets. Our results may advance our understanding of molecular mechanisms underlying HCC. The biomarkers may contribute to diagnosis in future clinical practice.

scholarly journals Normalized ImQCM: An Algorithm for Detecting Weak Quasi-Cliques in Weighted Graph with Applications in Gene Co-Expression Module Discovery in Cancers

2014 ◽  
Vol 13s3 ◽  
pp. CIN.S14021 ◽  
Author(s):  
Jie Zhang ◽  
Kun Huang
Keyword(s):  
Computing Time ◽  
Coexpression Network ◽  
Gene Coexpression Network ◽  
New Approach ◽  
Cancer Data ◽  
Network Analyses ◽  
Functional Relationships ◽  
Gene Coexpression ◽  
Gene Modules ◽  
Chromosomal Bands

In this paper, we present a new approach for mining weighted networks to identify densely connected modules such as quasi-cliques. Quasi-cliques are densely connected subnetworks in a network. Detecting quasi-cliques is an important topic in data mining, with applications such as social network study and biomedicine. Our approach has two major improvements upon previous work. The first is the use of local maximum edges to initialize the search in order to avoid excessive overlaps among the modules, thereby greatly reducing the computing time. The second is the inclusion of a weight normalization procedure to enable discovery of “subtle” modules with more balanced sizes. We carried out careful tests on multiple parameters and settings using two large cancer datasets. This approach allowed us to identify a large number of gene modules enriched in both biological functions and chromosomal bands in cancer data, suggesting potential roles of copy number variations (CNVs) involved in the cancer development. We then tested the genes in selected modules with enriched chromosomal bands using The Cancer Genome Atlas data, and the results strongly support our hypothesis that the coexpression in these modules are associated with CN Vs. While gene coexpression network analyses have been widely adopted in disease studies, most of them focus on the functional relationships of coexpressed genes. The relationship between coexpression gene modules and CNVs are much less investigated despite the potential advantage that we can infer from such relationship without genotyping data. Our new approach thus provides a means to carry out deep mining of the gene coexpression network to obtain both functional and genetic information from the expression data.

scholarly journals Weighted gene coexpression network analysis reveals hub genes involved in cholangiocarcinoma progression and prognosis

2019 ◽  
Vol 49 (10) ◽  
pp. 1195-1206 ◽  
Author(s):  
Aiping Tian ◽  
Ke Pu ◽  
Boxuan Li ◽  
Min Li ◽  
Xiaoguang Liu ◽  
...  
Keyword(s):  
Network Analysis ◽  
Coexpression Network ◽  
Gene Coexpression Network ◽  
Hub Genes ◽  
Gene Coexpression ◽  
Coexpression Network Analysis
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