Contents

## What is a topological overlap matrix?

Topological overlap matrix The topological overlap of two nodes reflects their similarity in terms of the commonality of the nodes they connect to. Note that in an unweighted network, the number of shared neighbors of nodes i and j is given by ∑u≠i,ja iu a uj .

## What is topological overlap matrix WGCNA?

WGCNA constructs two matrices, first it defines a correlation matrix up to a power beta so the degree distribution will fit a small-word network. This is why it defines the TOM matrix which uses the co-expression Adjacency matrix and build another adjacency matrix that considers topological similarity.

**What is an Eigengene?**

Filters. (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.

**What is Tom in WGCNA?**

Abstract I describe the “signed” Topological Overlap Matrix introduced in the WGCNA R package. 1 Review of TOM and signed vs. unsigned networks. The Topological Overlap Measure (TOM) was introduced in [1] to make networks less sensitive to spu- rious connections or to connections missing due to random noise.

### What do you mean by adjacency matrix of a graph?

3.3. The adjacency matrix [55, 56] is a matrix used to represent finite graphs. The values in the matrix show whether pairs of nodes are adjacent to each other in the graph structure. If the graph is undirected, then the adjacency matrix will be a symmetric one.

### 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 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 are module Eigengenes?**

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 a symmetric adjacency matrix indicate?

In graph theory and computer science, an adjacency matrix is a square matrix used to represent a finite graph. The elements of the matrix indicate whether pairs of vertices are adjacent or not in the graph. If the graph is undirected (i.e. all of its edges are bidirectional), the adjacency matrix is symmetric.

**What is adjacency matrix used for?**

**What is WGCNA used for?**

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.