Description. Calculates intramodular connectivity, i.e., connectivity of nodes to other nodes within the same module.
What is gene significance WGCNA?
WGCNA starts from the level of thousands of genes, identifies clinically interesting gene modules, and finally uses intramodular connectivity, gene significance (e.g. based on the correlation of a gene expression profile with a sample trait) to identify key genes in the disease pathways for further validation.
How do you choose a soft threshold in WGCNA?
To pick up one threshold use the pickSoftThreshold function, which calculates for each power if the network resembles to a scale-free graph. The power which produce a higher similarity with a scale-free network is the one you should use.
What is an Eigengene?
Eigengene meaning (genetics, mathematics) One of a set of right singular vectors of a genes x samples matrix that tabulates, e.g., the mRNA or gene expression of the genes across the samples. noun.
What is module membership in Wgcna?
The module membership (MM) was calculated by the WGCNA function signedKME that correlated the ME with gene expression values, so it quantified how close a gene was to a given module (Langfelder and Horvath, 2008).
What is a WGCNA module?
Weighted gene co-expression network analysis (WGCNA)6 is a popular systems biology method used to not only construct gene networks but also detect gene modules and identify the central players (i.e., hub genes) within modules.
What is WGCNA RNA seq?
WGCNA uses a series of correlations to identify sets of genes that are expressed together in your data set. This is a fairly intuitive approach to gene network analysis which can aid in interpretation of microarray & RNA-seq data.
What is FPKM value?
FPKM stands for Fragments Per Kilobase of transcript per Million mapped reads. In RNA-Seq, the relative expression of a transcript is proportional to the number of cDNA fragments that originate from it.
What is scale free topology in WGCNA?
•Scale Free Topology refers to. the frequency distribution of the. connectivity k. •p(k)=proportion of nodes that. have connectivity k.
What is the module Eigengene?
Module eigengene is defined as the first principal component of the expression matrix of the corresponding module. The calculation may fail if the expression data has too many missing entries.
What are hub genes?
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.
What does Coexpressed mean?
Filters. (genetics) To express together with another gene.
