This study explored the gene regulation profile of CDX-treated human glioma Hs683 cells.Using microarray technology and bioinformatics analyses the underlying molecular mechanism of action of CDX was evaluated by constructing gene regulation and protein-protein interaction co expression networks.CDX ...
To reveal the differences in the gene regulation of the drought response in sunflower varieties with contrasting drought tolerances, weighted gene coexpression network analysis (WGCNA) was performed on the 12,892 DEGs (Fig.8). Firstly, all the samples were clustered and it was found that the c...
Weighted gene coexpression network analysis (WGCNA) is a systems biology method that analyzes the gene expression patterns of multiple samples. This method aims to identify expression modules associated with specific traits or phenotypes and is an effective approach for studying gene regulatory networks ...
Co-expression networks were constructed using WGCNA(v 1.47) package in R75. After filtering genes with expression below 15, gene expression values were imported into WGCNA to construct co-expression modules using the automatic network construction function blockwiseModules with default settings, except ...
We used the Pcc method to construct a gene coexpression network in citrus, with a focus on the HLB response mechanism. The citrus gene coexpression network will be very useful for the citrus researchers to visualize the subnetworks specific for certain biological processes (such as carbohydrate ...
Human embryonic stem (ES) cells hold great promise for medicine and science. The transcriptome of human ES cells has been studied in detail in recent years. However, no systematic analysis has yet addressed whether gene expression in human ES cells may b
Co-expression networks revealed that transcripts of the neuroimmune systems interacted with neuronal-systems, both of which contribute to the pathology of brain disorders. However, only a few genes with expression changes were also identified as containing risk variants in genome-wide association studies...
Coexpression networks were constructed using the WGCNA (v1.47) package in R (Langfelder and Horvath 2008). First, we performed a cluster analysis of these samples using the flash Clust toolkit (Additional file 1: Fig. S11). Soft threshold is one of the most critical parameters, which mainly...
BMC Genomics (2018) 19:236 https://doi.org/10.1186/s12864-018-4632-y RESEARCH ARTICLE Open Access Gene co-expression networks in liver and muscle transcriptome reveal sex-specific gene expression in lambs fed with a mix of essential oils Marcella Sabino1, Victor Adriano Okstoft Carmelo2†,...
Generation of coding and non-coding gene co-expression networks To determine the possible functions of lncRNAs, we used aguilty-by-associationapproach. This approach identifies enriched functional annotations of protein-coding genes co-expressed with the lncRNAs, which allows inferring the biological proc...