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Identifying genes that interact to confer a biological function to an organism is one of the main goals of functional genomics. High-throughput technologies for assessment and quantification of genome-wide gene expression patterns have enabled systems-level analyses to infer pathways or networks of genes involved in different functions under many different conditions. Here, we leveraged the publicly available, information-rich RNA-Seq datasets of the model plant to construct a gene co-expression network, which was partitioned into clusters or modules that harbor genes correlated by expression. Gene ontology and pathway enrichment analyses were performed to assess functional terms and pathways that were enriched within the different gene modules. By interrogating the co-expression network for genes in different modules that associate with a gene of interest, diverse functional roles of the gene can be deciphered. By mapping genes differentially expressing under a certain condition in onto the co-expression network, we demonstrate the ability of the network to uncover novel genes that are likely transcriptionally active but prone to be missed by standard statistical approaches due to their falling outside of the confidence zone of detection. To our knowledge, this is the first co-expression network constructed using the entire mRNA-Seq datasets (>20,000) available at the NCBI SRA database. The developed network can serve as a useful resource for the research community to interrogate specific genes of interest within the network, retrieve the respective interactomes, decipher gene modules that are transcriptionally altered under certain condition or stage, and gain understanding of gene functions.
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http://dx.doi.org/10.1002/pld3.396 | DOI Listing |
Plant Physiol Biochem
December 2024
Key Laboratory of Herbage Improvement and Grassland Agroecosystems, Lanzhou University, Lanzhou, 730020, China; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, 730020, China; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China; Engineering Research Center of Grassland Industry, Ministry of Education, Gansu Tech Innovation Centre of Western China Grassland Industry, China. Electronic address:
Arbuscular mycorrhizal (AM) fungi are widely existing soil microorganisms that form symbiotic relationships with most terrestrial plants. They are important for enhancing adversity resistance, including resistance to disease and water stresses. Nevertheless, it is not clear whether the benefits can be maintained in regulating the occurrence of plant diseases under drought, flooding stress and during water restoration.
View Article and Find Full Text PDFCurr Res Food Sci
November 2024
Shandong Provincial Key Laboratory of Test Technology on Food Quality and Safety, Institute of Quality Standard and Testing Technology for Agro-Products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
Radish is an important vegetable worldwide, with wide medicinal functions and health benefits. The quality of radish, strongly affected by phytochemicals like flavonoids and glucosinolates, are quite different depending on the radish varieties. However, the comprehensive accumulation profiles of secondary metabolites and their molecular regulatory mechanisms in different radish cultivars remain unclear thus far.
View Article and Find Full Text PDFMediators Inflamm
December 2024
Department of Stomatology, School of Stomatology, The Third Affiliated Hospital, Xi'an Medical University, Xi'an, China.
This study aimed to investigate the molecular mechanisms of periodontitis and identify key immune-related biomarkers using machine learning and Mendelian randomization (MR). Differentially expressed gene (DEG) analysis was performed on periodontitis datasets GSE16134 and GSE10334 from the Gene Expression Omnibus (GEO) database, followed by weighted gene co-expression network analysis (WGCNA) to identify relevant gene modules. Various machine learning algorithms were utilized to construct predictive models, highlighting core genes, while MR assessed the causal relationships between these genes and periodontitis.
View Article and Find Full Text PDFPharmgenomics Pers Med
December 2024
Department of General Surgery, The Second Affiliated Hospital of Air Force Medical University, Xi'an, Shaanxi Province, People's Republic of China.
Objective: To identify key genes and potential molecular mechanisms associated with Hashimoto's thyroiditis (HT) to provide new insights for the development of diagnostic and therapeutic targets for this disease.
Methods: Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were conducted to identify the differentially expressed genes (DEGs) associated with HT. A protein-protein interaction (PPI) network was used to obtain hub genes, with CD27 emerging as the key gene in HT.
Food Chem X
December 2024
Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
The quality issues of ultra-high-temperature (UHT) milk, such as protein hydrolysis and aging gels throughout shelf life, are caused by proteases from psychrophilic bacteria. However, existing enzyme activity detection techniques have low sensitivity and cannot accomplish the detection of product deterioration caused by low enzyme activity. In this study, an attempt was made to analyze the relationship between enzymatically cleaved peptides and product quality using peptidomics techniques.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!