COMODO v2.0: COnserved MODules across Organims

Access previous version here

Zarrineh et al. 2010

COMODO v2.0 uses an objective selection criterium to identify conserved expression modules between three species (in contrast to its previous version which could only handle two species). The method uses as input microarray data and a gene homology map and provides as output pairs of conserved modules (Figure 1). COMODO v2.0 searches for module combinations in the species being compared, for which the number of sharing homologs is statiscally most significant relative to the size of the linked modules. COMODO v2.0 was fully written in Matlab and made available for academic use under the GPL (General Publuc License). In order to use COMODO v2.0, no Matlab license is requiered as the package contains the necessary libraries to run COMODO v2.0 using the free Matlab Compiler Runtime (MCR).


Figure 1. Detection of evolutionary conserved expression modules in a two-species comparison


1. Download COMODO here
2. Execute the downloaded .exe file, the COMODO v2.0 program will be extracted to the directory in which the .exe file resides
3. The Matlab Compiler Runtime will be installed, when asked for a .NET installation just press 'continue' (.NET is not needed for COMODO v2.0)
4. Run the unpacked COMODO executable


COMODO v2.0 requires four input files (see Figure 2):
1. Microarray expression data for species 1 (download sample file here)
2. Microarray expression data for species 2 (same format as file in 1)
3. Microarray expression data for species 3 (same format as file in 1)
4. Homologous gene sets (download sample file here)

The homology definition file (in 4) is a TAB delimited file with the following format:

Five parameters need to be defined in order to run COMODO:
- Initial highest threshold: Defines the maximal coexpression value in the gene-gene threshold matrix. Every coexpression value over this threshold is converted to the given value. It affects the selection of seed module step.
- Least acceptable threshold: Defines the lowest acceptable Pearson correlation coeficient during the seed module extension step.
- Searching step: Defines the stepwise change for relaxing the Paerson correlation coeficient threshold during the seed module extension step.
- Least initial core/total module size: Defines the minimum ratio of the core part over the total module size required for pairing up two seed modules one from each organism.
- Stopping core/total module size: Defines the minimum allowed ratio of the core part over the total module size. It is used as stopping criteria during the seed module extension step.

COMODO v2.0 generates a single output file (download sample file here)
The output consists of three TAB separated columns: MODULE_CORE_PART,ORGANISM1_SPECIFIC_GENES, ORGANISM2_SPECIFIC_GENES and ORGANISM3_SPECIFIC_GENES. The first column also indicates the homology links between genes across organisms in the format (gene1_organism1--gene1_organism2)(gene2_organism1--gene2_organism2) and so on.

Figure 2. Snapshot of the standalone application


This software was developed by the Bioinformatics lab of Prof. K. Marchal at the Centre for Microbial and Plant Genetics, Faculty of Bioscience Engineering (Katholieke Universiteit Leuven)

Dr. Peyman Zarrineh
Dr. Carolina Fierro
Dr. Aminael Sanchez-Rodriguez
Zahra Narimani
Nazanin Hosseinkhan
Prof. Ali Masoudi-Nejad
Prof. Kristof Engelen
Prof. Dr. Kathleen Marchal

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