Mimosa: mixture model of co-expression to detect modulators of regulatory interaction.
BACKGROUND
Functionally related genes tend to be correlated in their expression patterns across multiple conditions and/or tissue-types. Thus co-expression networks are often used to investigate functional groups of genes. In particular, when one of the genes is a transcription factor (TF), the co-expression-based interaction is interpreted, with caution, as a direct regulatory interaction. However, any particular TF, and more importantly, any particular regulatory interaction, is likely to be active only in a subset of experimental conditions. Moreover, the subset of expression samples where the regulatory interaction holds may be marked by presence or absence of a modifier gene, such as an enzyme that post-translationally modifies the TF. Such subtlety of regulatory interactions is overlooked when one computes an overall expression correlation.


RESULTS
Here we present a novel mixture modeling approach where a TF-Gene pair is presumed to be significantly correlated (with unknown coefficient) in an (unknown) subset of expression samples. The parameters of the model are estimated using a Maximum Likelihood approach. The estimated mixture of expression samples is then mined to identify genes potentially modulating the TF-Gene interaction. We have validated our approach using synthetic data and on four biological cases in cow, yeast, and humans.


CONCLUSIONS
While limited in some ways, as discussed, the work represents a novel approach to mine expression data and detect potential modulators of regulatory interactions.
Hansen
Matthew
M
Department of Genetics, Penn Center for Bioinformatics, University of Pennsylvania, Pennsylvania, USA.
Everett
Logan
L
Department of Genetics, Penn Center for Bioinformatics, University of Pennsylvania, Pennsylvania, USA.
Singh
Larry
L
Department of Genetics, Penn Center for Bioinformatics, University of Pennsylvania, Pennsylvania, USA.
Hannenhalli
Sridhar
S
Department of Genetics, Penn Center for Bioinformatics, University of Pennsylvania, Pennsylvania, USA.