Analyse co-expression gene modules with CEMItool


Identifying single changes in gene expression levels is a common analysis step after a microarray or RNA-Seq experiment. The expression levels of co-expressed genes can also be analyzed and visualized by gene co-expression networks (GCNs), which are undirected graphs used to represent co-expression relationships between pairs of genes across samples.


Dr. Helder Nakaya from Sao Paolo University has recently developed CEMItool, an easy-to-use method to automatically run gene co-expression analyses in R. Here, he describes the features provided by CEMItools.

Analyse your transcriptomic data for co-expression modules

The analysis of co-expression gene modules can help uncover the mechanisms underlying diseases and infection. CEMItool is a fast and easy-to-use Bioconductor package that unifies the discovery and the analysis of co-expression modules.


Among its features, CEMItool evaluates whether modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group, as well as it integrates transcriptomic data with interactome information, identifying the potential hubs on each network.


In addition, CEMiTool provides users with a novel unsupervised gene filtering method, and automated parameter selection for identifying modules. The tool then reports everything in HTML web pages with high-quality plots and interactive tables.

CEMItool features


Several functions can be run independently, or all at once using the cemitool function. Using a simple command line, CEMItool can generate a plot that displays the expression of each gene within a module.

CEMItool can generate a plot that displays the expression of each gene
Expression of each genes within a module


CEMItool can also determine which biological functions are associated with the module by performing an over representation analysis (ORA). For this command, a pathway list must be provided in the form of GMT file:


CEMItool can also determine which biological functions
Biological functions associated with the module.


Finally, interaction data, such as protein-protein interactions can be visualized in annotated module graphs:

Annotated graph showing interactions within a module
Annotated graph showing interactions within a module.


Overall, the CEMItool provides the following benefits:

  • Easy-to-use package, automating within a single R function (cemitool) the entire module discovery process – including gene filtering and functional analyses
  • Perform comprehensive modular analysis
  • Fully automated process

A comprehensive instruction guide for CEMItool is provided on Bioconductor : Link


Russo P, Ferreira G, Bürger M, Cardozo L and Nakaya H (2017). CEMiTool: Co-expression Modules identification Tool. R package version 1.1.1.