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Using Qualitative Probability in Reverse-Engineering Gene Regulatory Networks
March/April 2011 (vol. 8 no. 2)
pp. 326-334
ASCII Text
x 
 
Zina M. Ibrahim, Alioune Ngom, Ahmed Y. Tawfik, "Using Qualitative Probability in Reverse-Engineering Gene Regulatory Networks," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. 2, pp. 326-334, March/April, 2011.
 
 
BibTex
x
 
@article{ 10.1109/TCBB.2010.98,
author = {Zina M. Ibrahim and Alioune Ngom and Ahmed Y. Tawfik},
title = {Using Qualitative Probability in Reverse-Engineering Gene Regulatory Networks},
journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
volume = {8},
number = {2},
issn = {1545-5963},
year = {2011},
pages = {326-334},
doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.98},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - JOUR
JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics
TI - Using Qualitative Probability in Reverse-Engineering Gene Regulatory Networks
IS - 2
SN - 1545-5963
SP326
EP334
EPD - 326-334
A1 - Zina M. Ibrahim,
A1 - Alioune Ngom,
A1 - Ahmed Y. Tawfik,
PY - 2011
KW - Gene regulatory networks
KW - reverse-engineering genetic networks
KW - dynamic Bayesian networks
KW - qualitative probabilistic networks
KW - qualitative reasoning.
VL - 8
JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics
ER -
 
Zina M. Ibrahim, University of Windsor, Ontario
Alioune Ngom, University of Windsor, Ontario
Ahmed Y. Tawfik, French University in Egypt, Cairo
This paper demonstrates the use of qualitative probabilistic networks (QPNs) to aid Dynamic Bayesian Networks (DBNs) in the process of learning the structure of gene regulatory networks from microarray gene expression data. We present a study which shows that QPNs define monotonic relations that are capable of identifying regulatory interactions in a manner that is less susceptible to the many sources of uncertainty that surround gene expression data. Moreover, we construct a model that maps the regulatory interactions of genetic networks to QPN constructs and show its capability in providing a set of candidate regulators for target genes, which is subsequently used to establish a prior structure that the DBN learning algorithm can use and which 1) distinguishes spurious correlations from true regulations, 2) enables the discovery of sets of coregulators of target genes, and 3) results in a more efficient construction of gene regulatory networks. The model is compared to the existing literature using the known gene regulatory interactions of Drosophila Melanogaster.

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Index Terms:
Gene regulatory networks, reverse-engineering genetic networks, dynamic Bayesian networks, qualitative probabilistic networks, qualitative reasoning.
Citation:
Zina M. Ibrahim, Alioune Ngom, Ahmed Y. Tawfik, "Using Qualitative Probability in Reverse-Engineering Gene Regulatory Networks," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. 2, pp. 326-334, March-April 2011, doi:10.1109/TCBB.2010.98
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