Title: COMODO: an adaptive coclustering strategy to identify conserved coexpression modules between organisms
Authors: Peyman, Zarineh * ×
Fierro GutiƩrrez, Ana Carolina Elisa *
Sanchez Rodriguez, Aminael
De Moor, Bart
Engelen, Kristof
Marchal, Kathleen #
Issue Date: 10-Dec-2011
Publisher: Oxford University Press
Series Title: Nucleic Acids Research vol:39 issue:7 pages:E41-U45
Abstract: Increasingly large-scale expression compendia for different species are becoming available. By exploiting the modularity of the coexpression network, these compendia can be used to identify biological processes for which the expression behavior is conserved over different species. However, comparing module networks across species is not trivial. The definition of a biologically meaningful module is not a fixed one and changing the distance threshold that defines the degree of coexpression gives rise to different modules. As a result when comparing modules across species, many different partially overlapping conserved module pairs across species exist and deciding which pair is most relevant is hard. Therefore, we developed a method referred to as conserved modules across organisms (COMODO) that uses an objective selection criterium to identify conserved expression modules between two species. The method uses as input microarray data and a gene homology map and provides as output pairs of conserved modules and searches for the pair of modules for which the number of sharing homologs is statistically most significant relative to the size of the linked modules. To demonstrate its principle, we applied COMODO to study coexpression conservation between the two well-studied bacteria Escherichia coli and Bacillus subtilis. COMODO is available at:∼kmarchal/Supplementary_Information_Zarrineh_2010/comodo/index.html.
ISSN: 0305-1048
Publication status: published
KU Leuven publication type: IT
Appears in Collections:Electrical Engineering - miscellaneous
ESAT - STADIUS, Stadius Centre for Dynamical Systems, Signal Processing and Data Analytics
Centre of Microbial and Plant Genetics
* (joint) first author
× corresponding author
# (joint) last author

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