scholarly journals Application of weighted gene co‐expression network analysis (WGCNA) to identify novel key genes in diabetic nephropathy

2021 ◽  
Author(s):  
Zheng Wang ◽  
Xiaolei Chen ◽  
Chao Li ◽  
Wanxin Tang
Keyword(s):  
Diabetic Nephropathy ◽  
Network Analysis ◽  
Key Genes

scholarly journals Microarray analysis reveals an inflammatory transcriptomic signature in peripheral blood for sciatica

BMC Neurology ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yi Wang ◽  
Guogang Dai ◽  
Ling Jiang ◽  
Shichuan Liao ◽  
Jiao Xia
Keyword(s):  
Functional Analysis ◽  
Network Analysis ◽  
Peripheral Blood ◽  
Differentially Expressed ◽  
Healthy Controls ◽  
Toll Like Receptor ◽  
Qrt Pcr ◽  
Transcriptomic Signature ◽  
Transcriptional Changes ◽  
Key Genes

Abstract Background Although the pathology of sciatica has been studied extensively, the transcriptional changes in the peripheral blood caused by sciatica have not been characterized. This study aimed to characterize the peripheral blood transcriptomic signature for sciatica. Methods We used a microarray to identify differentially expressed genes in the peripheral blood of patients with sciatica compared with that of healthy controls, performed a functional analysis to reveal the peripheral blood transcriptomic signature for sciatica, and conducted a network analysis to identify key genes that contribute to the observed transcriptional changes. The expression levels of these key genes were assessed by qRT-PCR. Results We found that 153 genes were differentially expressed in the peripheral blood of patients with sciatica compared with that of healthy controls, and 131 and 22 of these were upregulated and downregulated, respectively. A functional analysis revealed that these differentially expressed genes (DEGs) were strongly enriched for the inflammatory response or immunity. The network analysis revealed that a group of genes, most of which are related to the inflammatory response, played a key role in the dysregulation of these DEGs. These key genes are Toll-like receptor 4, matrix metallopeptidase 9, myeloperoxidase, cathelicidin antimicrobial peptide, resistin and Toll-like receptor 5, and a qRT-PCR analysis validated the higher transcript levels of these key genes in the peripheral blood of patients with sciatica than in that of healthy controls. Conclusion We revealed inflammatory characteristics that serve as a peripheral blood transcriptomic signature for sciatica and identified genes that are essential for mRNA dysregulation in the peripheral blood of patients with sciatica.

scholarly journals Identification of Key Genes Affecting Porcine Fat Deposition Based on Co-Expression Network Analysis of Weighted Genes

2021 ◽  
Author(s):  
Kai Xing ◽  
Huatao Liu ◽  
Fengxia Zhang ◽  
Yibing Liu ◽  
Yong Shi ◽  
...  
Keyword(s):  
Network Analysis ◽  
Production Efficiency ◽  
Fat Deposition ◽  
Rna Seq ◽  
Genetic Studies ◽  
Gene Expression Matrix ◽  
Differential Gene ◽  
Key Genes ◽  
Strong Candidate ◽  
Molecular Regulatory Mechanisms

Abstract Background: Fat deposition is an important economic consideration for pig production. The amount of fat deposition in pigs seriously affects production efficiency, quality, and reproductive performance, while also affecting consumers' choice of pork. Weighted gene co-expression network analysis (WGCNA) has been shown to be effective in pig genetic studies. Therefore, this study aimed to identify modules that co-express genes associated with fat deposition in pigs (Songliao black and Landrace breeds) with extreme levels of backfat (high and low), and to identify the central genes in each of these modules. Results: We used RNA-seq of different pig tissues to construct a gene expression matrix consisting of 12 862 genes from 36 samples. Eleven co-expression modules were identified using WGCNA; the number of genes in these modules ranged from 39 to 3363. We found four co-expression modules were significantly correlated with backfat thickness. A total of 14 genes ( RAD9A , IGF2R , SCAP , TCAP , DGAT1 , GPS2 , IGF1 , MAPK8 , FABP , FABP5 , LEPR , UCP3 , APOF , and FASN ) were found to be related to fat deposition. Conclusions: RAD9A , TCAP , GPS2 , and APOF were found to be the key genes in the four modules according to the degree of gene connectivity. Combining the results of differential gene analysis, APOF was proposed as a strong candidate gene for body size traits. This study explores the key genes that regulate porcine fat deposition and lays the foundation for further research into the molecular regulatory mechanisms behind porcine fat deposition.

Integrated Bioinformatics and Machine Learning Algorithms Analyses Highlight Related Pathways and Genes Associated with Alzheimer's Disease

2021 ◽  
Vol 17 ◽  
Author(s):  
Hui Zhang ◽  
Qidong Liu ◽  
Xiaoru Sun ◽  
Yaru Xu ◽  
Yiling Fang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Network Analysis ◽  
Predictive Model ◽  
Differentially Expressed Genes ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Differentially Expressed ◽  
Diagnosis And Treatment ◽  
Ppi Network ◽  
Key Genes

Background: The pathophysiology of Alzheimer's disease (AD) is still not fully studied. Objective: This study aimed to explore the differently expressed key genes in AD and build a predictive model of diagnosis and treatment. Methods: Gene expression data of the entorhinal cortex of AD, asymptomatic AD, and control samples from the GEO database were analyzed to explore the relevant pathways and key genes in the progression of AD. Differentially expressed genes between AD and the other two groups in the module were selected to identify biological mechanisms in AD through KEGG and PPI network analysis in Metascape. Furthermore, genes with a high connectivity degree by PPI network analysis were selected to build a predictive model using different machine learning algorithms. Besides, model performance was tested with five-fold cross-validation to select the best fitting model. Results: A total of 20 co-expression gene clusters were identified after the network was constructed. Module 1 (in black) and module 2 (in royal blue) were most positively and negatively correlated with AD, respectively. Total 565 genes in module 1 and 215 genes in module 2, respectively, overlapped in two differentially expressed genes lists. They were enriched in the G protein-coupled receptor signaling pathway, immune-related processes, and so on. 11 genes were screened by using lasso logistic regression, and they were considered to play an important role in predicting AD samples. The model built by the support vector machine algorithm with 11 genes showed the best performance. Conclusion: This result shed light on the diagnosis and treatment of AD.

Identification of key genes of hesperidin in inhibition of breast cancer stem cells by functional network analysis

2021 ◽  
Vol 90 ◽  
pp. 107427
Author(s):  
Adam Hermawan ◽  
Annisa Khumaira ◽  
Muthi Ikawati ◽  
Herwandhani Putri ◽  
Riris Istighfari Jenie ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Stem Cells ◽  
Network Analysis ◽  
Cancer Stem Cells ◽  
Functional Network ◽  
Breast Cancer Stem Cells ◽  
Key Genes

scholarly journals SP455Identification of key lncRNAs contributing to diabetic nephropathy by gene co-repression network analysis

2019 ◽  
Vol 34 (Supplement_1) ◽  
Author(s):  
Shang Jing ◽  
Yanna dou ◽  
Cheng Genyang ◽  
Liu Dong ◽  
Xiao Jing ◽  
...  
Keyword(s):  
Diabetic Nephropathy ◽  
Network Analysis

Identification of key genes associated with overwintering in Anoplophora glabripennis larva using gene co‐expression network analysis

2020 ◽  
Author(s):  
Yabei Xu ◽  
Yurong Li ◽  
Qianqian Wang ◽  
Chunchun Zheng ◽  
Dongfang Zhao ◽  
...  
Keyword(s):  
Network Analysis ◽  
Anoplophora Glabripennis ◽  
Key Genes
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