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Inferring gene regulatory networks from multiple microarray datasets
Wang, Yong; Joshi, Trupti; Zhang, Xiang-Sun; Xu, Dong; Chen, Luonan
Source PublicationBIOINFORMATICS
AbstractMotivation: Microarray gene expression data has increasingly become the common data source that can provide insights into biological processes at a system-wide level. One of the major problems with microarrays is that a dataset consists of relatively few time points with respect to a large number of genes, which makes the problem of inferring gene regulatory network an ill-posed one. On the other hand, gene expression data generated by different groups worldwide are increasingly accumulated on many species and can be accessed from public databases or individual websites, although each experiment has only a limited number of time-points. Results: This paper proposes a novel method to combine multiple time-course microarray datasets from different conditions for inferring gene regulatory networks. The proposed method is called GNR (Gene Network Reconstruction tool) which is based on linear programming and a decomposition procedure. The method theoretically ensures the derivation of the most consistent network structure with respect to all of the datasets, thereby not only significantly alleviating the problem of data scarcity but also remarkably improving the prediction reliability. We tested GNR using both simulated data and experimental data in yeast and Arabidopsis. The result demonstrates the effectiveness of GNR in terms of predicting new gene regulatory relationship in yeast and Arabidopsis.
WOS Research AreaBiochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics
WOS SubjectBiochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability
WOS IDWOS:000241271000014
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Document Type期刊论文
Corresponding AuthorZhang, Xiang-Sun
Affiliation1.Osaka Sangyo Univ, Dept Elect Engn & Elect, Osaka 5748530, Japan
2.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100080, Peoples R China
3.Univ Missouri, Dept Comp Sci, Columbia, MO 65211 USA
4.Univ Missouri, Christopher S Bond Life Sci Ctr, Columbia, MO 65211 USA
5.Shanghai Univ, Inst Syst Biol, Shanghai 200444, Peoples R China
Recommended Citation
GB/T 7714
Wang, Yong,Joshi, Trupti,Zhang, Xiang-Sun,et al. Inferring gene regulatory networks from multiple microarray datasets[J]. BIOINFORMATICS,2006,22(19):2413-2420.
APA Wang, Yong,Joshi, Trupti,Zhang, Xiang-Sun,Xu, Dong,&Chen, Luonan.(2006).Inferring gene regulatory networks from multiple microarray datasets.BIOINFORMATICS,22(19),2413-2420.
MLA Wang, Yong,et al."Inferring gene regulatory networks from multiple microarray datasets".BIOINFORMATICS 22.19(2006):2413-2420.
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