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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
Bayesian analysis of signaling networks governing embryonic stem cell fate decisions
Bioinformatics, Volume 21, No. 6, Year 2005
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Description
Motivation: Signaling events that direct mouse embryonic stem (ES) cell self-renewal and differentiation are complex and accordingly difficult to understand in an integrated manner. We address this problem by adapting a Bayesian network learning algorithm to model proteomic signaling data for ES cell fate responses to external cues. Using this model we were able to characterize the signaling pathway influences as quantitative, logic-circuit type interactions. Our experimental data-set includes measurements for 28 signaling protein phosphorylation states across 16 different factorial combinations of cytokine and matrix stimuli as reported previously. Results: The Bayesian network modeling approach allows us to uncover previously reported signaling activities related to mouse ES cell self-renewal, such as the roles of LIF and STAT3 in maintaining undifferentiated ES cell populations. Furthermore, the network predicts novel influences such as between ERK phosphorylation and differentiation, or RAF phosphorylation and differentiated cell proliferation. Visualization of the influences detected by the Bayesian network provides intuition about the underlying physiology of the signaling pathways. We demonstrate that the Bayesian networks can capture the linear, nonlinear and multistate logic interactions that connect extracellular cues, intracellular signals and consequent cell functional responses. © The Author 2004. Published by Oxford University Press. All rights reserved.
Authors & Co-Authors
O'Meara, Wendy Prudhomme
United States, Cambridge
Massachusetts Institute of Technology
Daley, George Q.
United States, Cambridge
Massachusetts Institute of Technology
Lauffenburger, Douglas A.
United States, Ann Arbor
University of Michigan, Ann Arbor
Statistics
Citations: 105
Authors: 3
Affiliations: 3
Identifiers
Doi:
10.1093/bioinformatics/bti056
ISSN:
13674803
Study Approach
Quantitative