Contents
What are hub genes WGCNA?
Hub genes, defined as highly interconnected nodes in each module, are considered as functionally-important genes77. To identify the hub genes, the moduleEigengenes function was used for calculating the modules’ eigengenes, considered as the principal component of each module.
How do you identify a hub gene?
Identification and Validation of Hub Gene Hub genes are defined as genes with high correlation in candidate modules. High connectivity means that the connectivity ranked at top 10%. For example, if the module size was 1000, then the genes with top 100 were defined as the hub genes.
When do you use WGCNA?
Weighted correlation network analysis (WGCNA) can be used for finding clusters (modules) of highly correlated genes, for summarizing such clusters using the module eigengene or an intramodular hub gene, for relating modules to one another and to external sample traits (using eigengene network methodology), and for …
What does hub mean?
1 : the central part of a circular object (such as a wheel or propeller) spokes attached to the hub of the wheel. 2a : a center of activity : focal point The island is a major tourist hub. b : an airport or city through which an airline routes most of its traffic.
Are there any hub genes associated with ACC?
Further analysis identified four hub genes (i.e., TOP2A, TTK, CHEK1, and CENPA) from the module that were associated with ACC progression and prognosis. Thus, these hub genes may serve as candidate biomarkers of ACC in clinical treatment and contribute to a greater understanding of ACC progression.
How is weighted gene co-expression network analysis used?
Weighted gene co-expression network analysis (WGCNA) is a popular method in systems biology that can construct gene networks and detect gene modules ( Clarke et al., 2013; Yang et al., 2014; Lee et al., 2015; Goldman et al., 2017; Sun et al., 2017 ).
Why are genes found in the center of a regulation network?
Those genes found in the center of a regulation network usually exhibit more important functions. Thus, the degree of gene connectivity in one module can also be analyzed by the gene-gene interaction/regulation network, from which critical hub genes can be identified.
What are the genes in the Blue module?
Enrichment analysis revealed that genes in the blue module were mainly enriched in cell division, cell cycle, and DNA replication. Combined with the PPI and co-expression networks, we identified four hub genes (i.e., TOP2A, TTK, CHEK1, and CENPA) that were highly expressed in ACC and negatively correlated with OS.