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Enhancing cowpea wilt resistance: insights from gene coexpression network analysis with exogenous melatonin treatment
BackgroundCowpea wilt is a harmful disease caused by Fusarium oxysporum , leading to substantial losses in cowpea production. Melatonin reportedly...
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Coexpression Network Construction and Visualization from Transcriptomes Underlying ER Stress Responses
Dynamic gene expression changes are primary cellular reactions in response to most stresses and developmental cues in all organisms, including...
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Gene coexpression network during ontogeny in the yellow fever mosquito, Aedes aegypti
BackgroundThe behaviors and ontogeny of Aedes aegypti are closely related to the spread of diseases caused by dengue (DENV), chikungunya (CHIKV),...
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Weighted gene coexpression correlation network analysis reveals the potential molecular regulatory mechanism of citrate and anthocyanin accumulation between postharvest ‘Bingtangcheng’ and ‘Tarocco’ blood orange fruit
BackgroundOrganic acids and anthocyanins are the most important compounds for the flavor and nutritional quality of citrus fruit. However, there are...
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Coexpression enhances cross-species integration of single-cell RNA sequencing across diverse plant species
Single-cell RNA sequencing is increasingly used to investigate cross-species differences driven by gene expression and cell-type composition in...
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Comparative physiological and coexpression network analyses reveal the potential drought tolerance mechanism of peanut
BackgroundDrought stress has negative effects on plant growth and productivity. In this study, a comprehensive analysis of physiological responses...
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Gene-coexpression network analysis identifies specific modules and hub genes related to cold stress in rice
BackgroundWhen plants are subjected to cold stress, they undergo a series of molecular and physiological changes to protect themselves from injury....
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Comparative metabolomic and transcriptomic analysis reveals a coexpression network of the carotenoid metabolism pathway in the panicle of Setaria italica
BackgroundThe grains of foxtail millet are enriched in carotenoids, which endow this plant with a yellow color and extremely high nutritional value....
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Alzheimer’s disease rewires gene coexpression networks coupling different brain regions
Connectome studies have shown how Alzheimer’s disease (AD) disrupts functional and structural connectivity among brain regions. But the molecular...
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Robust normalization and transformation techniques for constructing gene coexpression networks from RNA-seq data
BackgroundConstructing gene coexpression networks is a powerful approach for analyzing high-throughput gene expression data towards module...
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Comparative transcriptome and coexpression network analysis reveals key pathways and hub candidate genes associated with sunflower (Helianthus annuus L.) drought tolerance
BackgroundDrought severely limits sunflower production especially at the seedling stage. To investigate the response mechanism of sunflowers to...
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Weighted gene coexpression correlation network analysis reveals a potential molecular regulatory mechanism of anthocyanin accumulation under different storage temperatures in ‘Friar’ plum
BackgroundFlesh is prone to accumulate more anthocyanin in postharvest ‘Friar’ plum ( Prunus salicina Lindl.) fruit stored at an intermediate...
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Gene Co-expression Network Analysis to Mine Genes Involved in Plant Secondary Metabolite Biosynthesis and Regulation
Plants produce diverse specialized metabolites (SMs) that do not participate in plant growth and development but help them adapt to various...
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Comparative Analysis of Core and Accessory Genes in Coexpression Network
Prokaryotes harbor a various proportion of accessory genes in their genomes. The integration of accessory functions with the core regulation network...
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Predicting synchronized gene coexpression patterns from fibration symmetries in gene regulatory networks in bacteria
BackgroundGene regulatory networks coordinate the expression of genes across physiological states and ensure a synchronized expression of genes in...
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Gene coexpression networks reveal molecular interactions underlying cichlid jaw modularity
BackgroundThe oral and pharyngeal jaw of cichlid fishes are a classic example of evolutionary modularity as their functional decoupling boosted...
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Coexpression network analysis reveals an MYB transcriptional activator involved in capsaicinoid biosynthesis in hot peppers
Plant biosynthesis involves numerous specialized metabolites with diverse chemical natures and biological activities. The biosynthesis of metabolites...
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Differential network analysis of bovine muscle reveals changes in gene coexpression patterns in response to changes in maternal nutrition
BackgroundCoexpression network analysis is a powerful tool to reveal transcriptional regulatory mechanisms, identify transcription factors, and...
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Network Analysis of Microarray Data
DNA microarrays are widely used to investigate gene expression. Even though the classical analysis of microarray data is based on the study of...
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A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships
BackgroundChromatin contacts are essential for gene-expression regulation; however, obtaining a high-resolution genome-wide chromatin contact map is...
