scholarly journals Integration of differential gene expression with weighted gene correlation network analysis identifies genes whose expression is remodeled throughout physiological aging in mouse tissues

2021 ◽  
Author(s):  
Margarida Ferreira ◽  
Stephany Francisco ◽  
Ana R. Soares ◽  
Ana Nobre ◽  
Miguel Pinheiro ◽  
...  
Keyword(s):  
Gene Expression ◽  
Network Analysis ◽  
Differential Gene Expression ◽  
Functional Enrichment ◽  
Correlation Network ◽  
Physiological Aging ◽  
Mouse Tissues ◽  
Gene Correlation ◽  
Differential Gene ◽  
The Brain

AbstractGene expression alterations occur in all mouse tissues during aging, but recent works highlight minor rather than major dysregulation amplitude for most genes, questioning whether differentially expressed genes on their own provide deep insight into aging biology. To clarify this issue, we have combined differential gene expression with weighted gene correlation network analysis (WGCNA) to identify expression signatures accounting for the pairwise relations between gene expression profiles and the cumulative effect of genes with small fold- changes during aging in the brain, heart, liver, skeletal muscle, and pancreas of C57BL/6 mice. Functional enrichment analysis of the overlap of genes identified in both approaches showed that immunity-related responses, mitochondrial energy metabolism, tissue regeneration and detoxification are prominently altered in the brain, heart, muscle, and liver, respectively, reflecting an age-related global loss of tissue function. While data showed little overlap among the age-dysregulated genes between tissues, aging triggered common biological processes in distinct tissues, particularly proteostasis-related pathways, which we highlight as important features of murine tissue physiological aging.

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 Response network analysis of differential gene expression in human epithelial lung cells during avian influenza infections

2010 ◽  
Vol 11 (1) ◽  
pp. 170 ◽  
Author(s):  
Ken Tatebe ◽  
Ahmet Zeytun ◽  
Ruy M Ribeiro ◽  
Robert Hoffmann ◽  
Kevin S Harrod ◽  
...  
Keyword(s):  
Gene Expression ◽  
Network Analysis ◽  
Avian Influenza ◽  
Differential Gene Expression ◽  
Lung Cells ◽  
Response Network ◽  
Differential Gene ◽  
Epithelial Lung Cells

scholarly journals Vascular Genomics of the Human Brain

2002 ◽  
Vol 22 (3) ◽  
pp. 245-252 ◽  
Author(s):  
Eric V. Shusta ◽  
Ruben J. Boado ◽  
Gary W. Mathern ◽  
William M. Pardridge
Keyword(s):  
Gene Expression ◽  
Human Brain ◽  
Differential Gene Expression ◽  
Molecular Transport ◽  
Brain Diseases ◽  
Microvascular Endothelium ◽  
Whole Brain ◽  
Differential Gene ◽  
Brain Microvasculature ◽  
The Brain

The microvasculature of the human brain plays an important role in the development and maintenance of the central nervous system and in the pathogenesis of brain diseases, and is the site of differential gene expression within the brain. However, human brain microvascular-specific genes may not be detected in whole-brain gene microarray because the volume of the brain microvascular endothelium is relatively small (0.1%) compared with the whole brain. Therefore, the differential gene expression within the human brain microvasculature was evaluated using suppression subtractive hybridization with RNA isolated from human brain microvessels. Gene identification was restricted to the first 71 clones that were differentially expressed at the brain microvasculature. Twenty of these were genes encoding proteins with known function that were involved in angiogenesis, neurogenesis, molecular transport, and maintenance of endothelial tight junctions or the cytoskeleton. Eighteen genes coding for proteins of an unknown function were identified, including five genes containing satellite DNA sequences. The results provide the initial outline of the genomics of the human brain microvasculature, and have implications for the identification of both targets for brain-specific drug transport and changes in microvascular gene expression in brain diseases.

scholarly journals Cognitive Stimulation Induces Differential Gene Expression in Octopus vulgaris: The Key Role of Protocadherins

Biology ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 196
Author(s):  
Valeria Maselli ◽  
Gianluca Polese ◽  
Al-Sayed Al-Soudy ◽  
Maria Buglione ◽  
Anna Di Cosmo
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Adult Neurogenesis ◽  
Control Cell ◽  
Enriched Environment ◽  
Cognitive Stimulation ◽  
Octopus Vulgaris ◽  
Brain Areas ◽  
Differential Gene ◽  
The Brain

Octopuses are unique invertebrates, with sophisticated and flexible behaviors controlled by a high degree of brain plasticity, learning, and memory. Moreover, in Octopus vulgaris, it has been demonstrated that animals housed in an enriched environment show adult neurogenesis in specific brain areas. Firstly, we evaluated the optimal acclimatization period needed for an O. vulgaris before starting a cognitive stimulation experiment. Subsequently, we analyzed differential gene expression in specific brain areas in adult animals kept in tested (enriched environment), wild (naturally enriched environment), and control conditions (unenriched environment). We selected and sequenced three protocadherin genes (PCDHs) involved in the development and maintenance of the nervous system; three Pax genes that control cell specification and tissue differentiation; the Elav gene, an earliest marker for neural cells; and the Zic1 gene, involved in early neural formation in the brain. In this paper, we evaluated gene expression levels in O. vulgaris under different cognitive stimulations. Our data shows that Oct-PCDHs genes are upregulated in the learning and lower motor centers in the brain of both tested and wild animals (higher in the latter). Combining these results with our previous studies on O. vulgaris neurogenesis, we proposed that PCDH genes may be involved in adult neurogenesis processes, and related with their cognitive abilities.

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 Developmental Alcohol Exposure in Drosophila: Effects on Adult Phenotypes and Gene Expression in the Brain

2021 ◽  
Vol 12 ◽  
Author(s):  
Sneha S. Mokashi ◽  
Vijay Shankar ◽  
Rebecca A. MacPherson ◽  
Rachel C. Hannah ◽  
Trudy F. C. Mackay ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Genetic Model ◽  
Alcohol Exposure ◽  
Behavioral Changes ◽  
Glutathione Metabolism ◽  
Human Populations ◽  
Fetal Alcohol ◽  
Differential Gene ◽  
The Brain

Fetal alcohol exposure can lead to developmental abnormalities, intellectual disability, and behavioral changes, collectively termed fetal alcohol spectrum disorder (FASD). In 2015, the Centers for Disease Control found that 1 in 10 pregnant women report alcohol use and more than 3 million women in the USA are at risk of exposing their developing fetus to alcohol. Drosophila melanogaster is an excellent genetic model to study developmental effects of alcohol exposure because many individuals of the same genotype can be reared rapidly and economically under controlled environmental conditions. Flies exposed to alcohol undergo physiological and behavioral changes that resemble human alcohol-related phenotypes. Here, we show that adult flies that developed on ethanol-supplemented medium have decreased viability, reduced sensitivity to ethanol, and disrupted sleep and activity patterns. To assess the effects of exposure to alcohol during development on brain gene expression, we performed single cell RNA sequencing and resolved cell clusters with differentially expressed genes which represent distinct neuronal and glial populations. Differential gene expression showed extensive sexual dimorphism with little overlap between males and females. Gene expression differences following developmental alcohol exposure were similar to previously reported differential gene expression following cocaine consumption, suggesting that common neural substrates respond to both drugs. Genes associated with glutathione metabolism, lipid transport, glutamate and GABA metabolism, and vision feature in sexually dimorphic global multi-cluster interaction networks. Our results provide a blueprint for translational studies on alcohol-induced effects on gene expression in the brain that may contribute to or result from FASD in human populations.

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