Weighted gene correlation network analysis identifies RSAD2, HERC5, and CCL8 as prognostic candidates for breast cancer

2019 ◽  
Vol 235 (1) ◽  
pp. 394-407 ◽  
Author(s):  
Jianing Tang ◽  
Qian Yang ◽  
Qiuxia Cui ◽  
Dan Zhang ◽  
Deguang Kong ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Network Analysis ◽  
Correlation Network ◽  
Gene Correlation

scholarly journals Integrative Identification of Hub Genes Associated With Immune Cells in Atrial Fibrillation Using Weighted Gene Correlation Network Analysis

2021 ◽  
Vol 7 ◽  
Author(s):  
Tao Yan ◽  
Shijie Zhu ◽  
Miao Zhu ◽  
Chunsheng Wang ◽  
Changfa Guo
Keyword(s):  
Atrial Fibrillation ◽  
Network Analysis ◽  
Molecular Mechanism ◽  
Immune Cells ◽  
Bioinformatics Analysis ◽  
Functional Enrichment ◽  
Correlation Network ◽  
Hub Genes ◽  
Qrt Pcr ◽  
Gene Correlation

Background: Atrial fibrillation (AF) is the most common tachyarrhythmia in the clinic, leading to high morbidity and mortality. Although many studies on AF have been conducted, the molecular mechanism of AF has not been fully elucidated. This study was designed to explore the molecular mechanism of AF using integrative bioinformatics analysis and provide new insights into the pathophysiology of AF.Methods: The GSE115574 dataset was downloaded, and Cibersort was applied to estimate the relative expression of 22 kinds of immune cells. Differentially expressed genes (DEGs) were identified through the limma package in R language. Weighted gene correlation network analysis (WGCNA) was performed to cluster DEGs into different modules and explore relationships between modules and immune cell types. Functional enrichment analysis was performed on DEGs in the significant module, and hub genes were identified based on the protein-protein interaction (PPI) network. Hub genes were then verified using quantitative real-time polymerase chain reaction (qRT-PCR).Results: A total of 2,350 DEGs were identified and clustered into eleven modules using WGCNA. The magenta module with 246 genes was identified as the key module associated with M1 macrophages with the highest correlation coefficient. Three hub genes (CTSS, CSF2RB, and NCF2) were identified. The results verified using three other datasets and qRT-PCR demonstrated that the expression levels of these three genes in patients with AF were significantly higher than those in patients with SR, which were consistent with the bioinformatic analysis.Conclusion: Three novel genes identified using comprehensive bioinformatics analysis may play crucial roles in the pathophysiological mechanism in AF, which provide potential therapeutic targets and new insights into the treatment and early detection of AF.

scholarly journals Identification of key genes in ruptured atherosclerotic plaques by weighted gene correlation network analysis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Bao-Feng Xu ◽  
Rui Liu ◽  
Chun-Xia Huang ◽  
Bin-Sheng He ◽  
Guang-Yi Li ◽  
...  
Keyword(s):  
Network Analysis ◽  
Correlation Network ◽  
Atherosclerotic Plaques ◽  
Gene Correlation ◽  
Key Genes

scholarly journals Weighted gene correlation network analysis identifies microenvironment-related genes signature as prognostic candidate for Grade II/III glioma

Aging ◽  
2020 ◽  
Vol 12 (21) ◽  
pp. 22122-22138
Author(s):  
Yong Li ◽  
Gang Deng ◽  
Huikai Zhang ◽  
Yangzhi Qi ◽  
Lun Gao ◽  
...  
Keyword(s):  
Network Analysis ◽  
Correlation Network ◽  
Gene Correlation ◽  
Grade Ii

scholarly journals Co-expression of key gene modules and pathways of human breast cancer cell lines

2019 ◽  
Vol 39 (7) ◽  
Author(s):  
Yadong Wu ◽  
Feng liu ◽  
Siyang Luo ◽  
Xinhai Yin ◽  
Dengqi He ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Network Analysis ◽  
Cell Lines ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Correlation Network ◽  
Breast Cancer Cell Lines ◽  
Hub Genes ◽  
Weighted Correlation

Abstract Breast cancer (BC) is the most common leading cause of cancer-related death in women worldwide. Gene expression profiling analysis for human BCs has been studied previously. However, co-expression analysis for BC cell lines is still devoid to date. The aim of the study was to identify key pathways and hub genes that may serve as a biomarker for BC and uncover potential molecular mechanism using weighted correlation network analysis. We analyzed microarray data of BC cell lines (GSE 48213) listed in the Gene Expression Omnibus database. Gene co-expression networks were used to construct and explore the biological function in hub modules using the weighted correlation network analysis algorithm method. Meanwhile, Gene ontology and KEGG pathway analysis were performed using Cytoscape plug-in ClueGo. The network of the key module was also constructed using Cytoscape. A total of 5000 genes were selected, 28 modules of co-expressed genes were identified from the gene co–expression network, one of which was found to be significantly associated with a subtype of BC lines. Functional enrichment analysis revealed that the brown module was mainly involved in the pathway of the autophagy, spliceosome, and mitophagy, the black module was mainly enriched in the pathway of colorectal cancer and pancreatic cancer, and genes in midnightblue module played critical roles in ribosome and regulation of lipolysis in adipocytes pathway. Three hub genes CBR3, SF3B6, and RHPN1 may play an important role in the development and malignancy of the disease. The findings of the present study could improve our understanding of the molecular pathogenesis of breast cancer.

scholarly journals Periostin Contributes to Immunoglobulin a Nephropathy by Promoting the Proliferation of Mesangial Cells: A Weighted Gene Correlation Network Analysis

2021 ◽  
Vol 11 ◽  
Author(s):  
Jingkui Wu ◽  
Qisheng Lin ◽  
Shu Li ◽  
Xinghua Shao ◽  
Xuying Zhu ◽  
...  
Keyword(s):  
Network Analysis ◽  
Mesangial Cells ◽  
Immunoglobulin A ◽  
Kidney Tissue ◽  
B Cell Lymphoma ◽  
Correlation Network ◽  
Healthy Controls ◽  
Immunoglobulin A Nephropathy ◽  
Variable Expression ◽  
Gene Correlation

Immunoglobulin A nephropathy (IgAN) is a known cause of end-stage kidney disease, but the pathogenesis and factors affecting prognosis are not fully understood. In the present study, we carried out weighted gene correlation network analysis (WGCNA) to identify hub genes related to the occurrence of IgAN and validated candidate genes in experiments using mouse mesangial cells (MMCs) and clinical specimens (kidney tissue from IgAN patients and healthy controls). We screened the GSE37460 and GSE104948 differentially expressed genes common to both datasets and identified periostin (POSTN) as one of the five key genes using the cytoHubba plugin of Cytoscape software and by receiver-operating characteristic curve analysis. The top 25% of genes in the GSE93798 dataset showing variable expression between IgAN and healthy tissue were assessed by WGCNA. The royalblue module in WGCNA was closely related to creatinine and estimated glomerular filtration rate (eGFR) in IgAN patients. POSTN had very high module membership and gene significance values for creatinine (0.82 and 0.66, respectively) and eGFR (0.82 and −0.67, respectively), indicating that it is a co-hub gene. In MMCs, POSTN was upregulated by transforming growth factor β1, and stimulation of MMCs with recombinant POSTN protein resulted in an increase in the level of proliferating cell nuclear antigen (PCNA) and a decrease in that of B cell lymphoma-associated X protein, which were accompanied by enhanced MMC proliferation. POSTN gene knockdown had the opposite effects. Immunohistochemical analysis of kidney tissue specimens showed that POSTN and PCNA levels were elevated, whereas the rate of apoptosis was reduced in IgAN patients relative to healthy controls. POSTN level in the kidney tissue of IgAN patients was positively correlated with creatinine level and negatively correlated with eGFR. Thus, POSTN promotes the proliferation of MCs to promote renal dysfunction in IgAN.

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