What is differential coexpression?

Differential coexpression—the alteration of gene coexpression patterns observed in different biological conditions—has been proposed to be a mechanism for revealing rewiring of transcription regulatory networks.

What is coexpression network analysis?

Weighted gene co-expression network analysis (WGCNA) is a bioinformatics application for exploring the relationships between different gene sets (modules), or between gene sets and clinical features (Langfelder and Horvath, 2008).

How is gene coexpression measured?

One method to infer gene function and gene–disease associations from genome-wide gene expression is co-expression network analysis (Figure 1), an approach that constructs networks of genes with a tendency to co-activate across a group of samples and subsequently interrogates and analyses this network.

What is differential network analysis?

A differential network analysis is considered when gene expression samples are collected from two distinct populations or “groups”. The analysis compares the set of inter-connections of genes between the groups. Additionally, the existence of gene pathways is assumed.

What is differential gene expression quizlet?

differential gene expression. the process by which cells become different from one another based upon the unique combo of genes that are active or expressed.

What is transcriptional data?

Transcription creates a text-based version of any original audio or video recording. Puts qualitative data and information into a text-based format. Makes data easier to analyze and share. Allows researchers to become more immersed into the data they collect.

What is the meaning of co-expression?

Filters. (genetics) The simultaneous expression of two or more genes. noun.

What does Coexpressed mean?

Filters. (genetics) To express together with another gene.

What is a gene module?

A gene module is defined as a set of coexpressed genes to which the same set of transcription factors binds.

How do you cite cytoscape?

Please cite the original Cytoscape paper when you use Cytoscape. This is critical to sustaining our federal funding. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T.

Which best defines differential gene expression?

Differential gene expression. The concept that all cells in the body have the same genome, but express different parts on it (“differential expression”) depending on cell type and tissue. Differential transcription. Difference in protein production.

How long does it take to do differential coexpression analysis?

This example illustrates the workflow of downloading gene expression data from GEO and identifying differentially coexpressed links (DCLs) and differentially coexpressed genes (DCGs). Analysis of all the genes (6104) will take about 20 minutes on a computer with 8 cores and 16GB RAM.

Why are differential regulatory analysis based on coexpression?

These efforts are aiming to transform underlying genomic information into valuable knowledges in biological and medical research fields.

How are counts used in differential expression analysis?

The count data used for differential expression analysis represents the number of sequence reads that originated from a particular gene. The higher the number of counts, the more reads associated with that gene, and the assumption that there was a higher level of expression of that gene in the sample.

How are DCLS assembled into a differential coexpression network?

DCLs are a list of differentially co-expressed gene pairs and can be assembled into a differential coexpression network. The network is scale-free but not smallworld (Hsu et al., 2017). The network can be visualized and analyzed using igraph ( https://cran.r-project.org/web/packages/igraph/index.html ).