In this study, we combined fruit placenta transcriptome data with weighted gene coexpression network analysis (WGCNA) to generate coexpression networks. A capsaicinoid-related gene module was identified in which the MYB transcription factor CaMYB48 plays a critical role in regulating capsaicinoid in ...
Zhang J, Zheng H, Li Y, Li H, Liu X, Qin H, Dong L and Wang D. Coexpression network analysis of the genes regulated by two types of resis- tance responses to powdery mildew in wheat. Sci Rep 2016; 6: 23805.Zhang JC, Zheng HY, Li YW, Li HJ, Liu X, Qin HJ, Dong LL, ...
Differential analysis of gene expression data, which is focused on identifying up- or downregulated genes, ignores many relationships between genes affected by miRNA-142 overexpression in a cell. Thus, we applied a correlation network model to identify the coexpressed genes and to study the impact ...
For computational reasons, the network analysis is often restricted to a subset of genes (e.g. the 4000 most varying genes). As we will detail below, each co-expression network corresponds to an adjacency matrix. The adjacency matrix encodes the connection strength between each pair of nodes....
Construction and analysis of co-expression module We use R-packet WGCNA for co-expression-network analysis [94]. The imported data were the FPKM values of all genes, and all low-expression genes were removed (FPKM < 1 in each treatment; we believed that the gene was not expressed), ...
Weighted gene coexpression network analysis The WGCNA R package was used to construct a coexpression network of all 12,892 DEGs. [36]. Poorly representative samples were removed using the stereotree static function. The β value was determined based on the scale-free topological fit index (R2...
Jong, AmbroseZhou, YanHongHuang, ShengHeYang ZW, Jiang YH, Ma C, Silvestri G, Bosinger SE, et al. (2016) Coexpression Network Analysis of Benign and Malignant Phenotypes of SIV-infected Sooty Mangabey and Rhesus Macaque. PLoS One.
picking invertebrates such as shrimp/insects from the soft lake bottom [40].C. horeiis the most specialised fry-eater in the Tropheini with a terminal mouth andL. dardenniiis an omnivore [57]. We used weighted gene coexpression network analysis (WGCNA) to identify major coexpression modules...
In this study, we used RNA-seq technology and weighted gene coexpression network analysis (WGCNA) were performed. The results showed 4 key modules were closely related to the physiological response of A. cicer. L. to salt stress. The differentially expressed genes (DEGs) of key modules were ...
Therefore, we conducted a gene coexpression network (GCN) analysis to analyze the genomic system of NBL stages 4 and 4S. Usually, when comparing two different tissues or conditions, a gene expression analysis, such as DESeq2, is performed. However, this method compares differences in a single...