https://scholars.lib.ntu.edu.tw/handle/123456789/463846
標題: | A robust correlation estimator and nonlinear recurrent model to infer genetic interactions in Saccharomyces cerevisiae and pathways of pulmonary disease in Homo sapiens | 作者: | Chuang, C.-L. Chen, C.-M. Wong, W.-S. Tsai, K.-N. Chan, E.-C. JOE-AIR JIANG |
公開日期: | 2009 | 卷: | 98 | 期: | 3 | 起(迄)頁: | 160-175 | 來源出版物: | BioSystems | 摘要: | In order to identify genes involved in complex diseases, it is crucial to study the genetic interactions at the systems biology level. By utilizing modern high throughput microarray technology, it has become feasible to obtain gene expressions data and turn it into knowledge that explains the regulatory behavior of genes. In this study, an unsupervised nonlinear model was proposed to infer gene regulatory networks on a genome-wide scale. The proposed model consists of two components, a robust correlation estimator and a nonlinear recurrent model. The robust correlation estimator was used to initialize the parameters of the nonlinear recurrent curve-fitting model. Then the initialized model was used to fit the microarray data. The model was used to simulate the underlying nonlinear regulatory mechanisms in biological organisms. The proposed algorithm was applied to infer the regulatory mechanisms of the general network in Saccharomyces cerevisiae and the pulmonary disease pathways in Homo sapiens. The proposed algorithm requires no prior biological knowledge to predict linkages between genes. The prediction results were checked against true positive links obtained from the YEASTRACT database, the TRANSFAC database, and the KEGG database. By checking the results with known interactions, we showed that the proposed algorithm could determine some meaningful pathways, many of which are supported by the existing literature. ? 2009 Elsevier Ireland Ltd. All rights reserved. |
URI: | https://scholars.lib.ntu.edu.tw/handle/123456789/463846 | DOI: | 10.1016/j.biosystems.2009.05.013 | SDG/關鍵字: | algorithm; correlation; database; gene expression; hominid; modeling; respiratory disease; yeast; article; bioinformatics; DNA microarray; fungal genetics; gene interaction; gene regulatory network; genetic algorithm; human; lung disease; mathematical model; Mycobacterium tuberculosis; nonhuman; nonlinear system; prediction; Saccharomyces cerevisiae; simulation; Epistasis, Genetic; Genes, Fungal; Humans; Lung Diseases; Models, Theoretical; Saccharomyces cerevisiae; Homo sapiens; Saccharomyces cerevisiae |
顯示於: | 醫學工程學研究所 |
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