Martial Sankar, Karen S. Osmont, Jakub Rolcik, Bojan Gujas, Danuse Tarkowska, Miroslav Strnad
BIOINFORMATICS
doi: 10.1093/bioinformatics/btr158:
,
2011
Keywords:
Abstract:
Motivation: Hormone pathway interactions are crucial in shaping
plant development, such as synergism between the auxin and
brassinosteroid pathways in cell elongation. Both hormone pathways
have been characterized in detail, revealing several feedback loops.
The complexity of this network, combined with a shortage of kinetic
data, renders its quantitative analysis virtually impossible at present.
Results: As a first step towards overcoming these obstacles, we
analyzed the network using a Boolean logic approach to build models
of auxin and brassinosteroid signaling, and their interaction. To
compare these discrete dynamic models across conditions, we
transformed them into qualitative continuous systems, which predict
network component states more accurately and can accommodate
kinetic data as they become available. To this end, we developed an
extension for the SQUAD software, allowing semi-quantitative
analysis of network states. Contrasting the developmental output
depending on cell type-specific modulators enabled us to identify a
most parsimonious model, which explains initially paradoxical mutant
phenotypes and revealed a novel physiological feature.
Availability: The package SQUADD is freely available via the Bioconductor
repository at : http://www.bioconductor.org/help/biocviews/
release/bioc/html/SQUADD.html.
IEB authors: Miroslav Strnad
Čeština
English