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Exploiting binary abstractions in deciphering gene interactions

Title
Exploiting binary abstractions in deciphering gene interactions
Authors
Yoon S.Garg A.Chung E.-Y.Park H.S.Park W.Y.De Micheli G.
Ewha Authors
박현석
SCOPUS Author ID
박현석scopus
Issue Date
2006
Journal Title
Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings
ISSN
0589-1019JCR Link
Citation
pp. 5858 - 5863
Indexed
SCOPUS scopus
Abstract
We consider computationally reconstructing gene regulatory networks on top of the binary abstraction of gene expression state information. Unlike previous Boolean network approaches, the proposed method does not handle noisy gene expression values directly. Instead, two-valued "hidden state" information is derived from gene expression profiles using a robust statistical technique, and a gene interaction network is inferred from this hidden state information. In particular, we exploit Espresso, a well-known 2-level Boolean logic optimizer in order to determine the core network structure. The resulting gene interaction networks can be viewed as dynamic Bayesian networks, which have key advantages over more conventional Bayesian networks in terms of biological phenomena that can be represented. The authors tested the proposed method with a time-course gene expression data set from microarray experiments on anti-cancer drugs doxorubicin and paclitaxel. A gene interaction network was produced by our method, and the identified genes were validated with a public annotation database. The experimental studies we conducted suggest that the proposed method inspired by engineering systems can be a very effective tool to decipher complex gene interactions in living systems. © 2006 IEEE.
DOI
10.1109/IEMBS.2006.260194
ISBN
1424400325; 9781424400324
Appears in Collections:
엘텍공과대학 > 컴퓨터공학과 > Journal papers
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