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Signaling network prediction by the Ontology Fingerprint enhanced Bayesian network

Qin, T and Tsoi, LC and Sims, KJ and Lu, X and Zheng, WJ (2012) Signaling network prediction by the Ontology Fingerprint enhanced Bayesian network. BMC Systems Biology, 6 (SUPPL3).

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Abstract

Background: Despite large amounts of available genomic and proteomic data, predicting the structure and response of signaling networks is still a significant challenge. While statistical method such as Bayesian network has been explored to meet this challenge, employing existing biological knowledge for network prediction is difficult. The objective of this study is to develop a novel approach that integrates prior biological knowledge in the form of the Ontology Fingerprint to infer cell-type-specific signaling networks via data-driven Bayesian network learning; and to further use the trained model to predict cellular responses.Results: We applied our novel approach to address the Predictive Signaling Network Modeling challenge of the fourth (2009) Dialog for Reverse Engineering Assessment's and Methods (DREAM4) competition. The challenge results showed that our method accurately captured signal transduction of a network of protein kinases and phosphoproteins in that the predicted protein phosphorylation levels under all experimental conditions were highly correlated (R2 = 0.93) with the observed results. Based on the evaluation of the DREAM4 organizer, our team was ranked as one of the top five best performers in predicting network structure and protein phosphorylation activity under test conditions.Conclusions: Bayesian network can be used to simulate the propagation of signals in cellular systems. Incorporating the Ontology Fingerprint as prior biological knowledge allows us to efficiently infer concise signaling network structure and to accurately predict cellular responses. © 2012 Qin et al.; licensee BioMed Central Ltd.


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Details

Item Type: Article
Status: Published
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Qin, T
Tsoi, LC
Sims, KJ
Lu, Xxinghua@pitt.eduXINGHUA
Zheng, WJ
Date: 17 December 2012
Date Type: Publication
Journal or Publication Title: BMC Systems Biology
Volume: 6
Number: SUPPL3
DOI or Unique Handle: 10.1186/1752-0509-6-s3-s3
Schools and Programs: School of Medicine > Biomedical Informatics
Refereed: Yes
Date Deposited: 02 Dec 2016 14:55
Last Modified: 21 Feb 2019 01:55
URI: http://d-scholarship.pitt.edu/id/eprint/29789

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