A Nonlinear Model and an Optimization Algorithm to Infer Genetic Interactions

Author

Chen, Chung-Ming ; Chuang, Cheng-Long ; Lee, Chi ; Wang, Chia-Chang ; Shieh, Grace S.

Author_Institution

Inst. of Biomed. Eng., Nat. Taiwan Univ., Taipei, Taiwan

fYear

2009

fDate

17-19 Oct. 2009

Firstpage

1

Lastpage

4

Abstract

An S-shape model and an optimization algorithm (GASA) are developed to infer genetic interactions and transcriptional regulation of a few genes simultaneously using microarray gene expression data (MGED). GASA consists of a genetic algorithm and a simulated annealing (SA) algorithm, which is enhanced by a steepest gradient descent algorithm to avoid being trapped in local minimum. An application of GASA is demonstrated, in which a subnetwork of human T-cell apoptosis is inferred. Several predicted interactions are supported by literature.

Keywords

cellular biophysics; genetic algorithms; genetics; molecular biophysics; optimisation; simulated annealing; S-shape model; genetic interactions; human T-cell apoptosis; microarray gene expression data; nonlinear model; optimization algorithm; simulated annealing algorithm; steepest gradient descent algorithm; transcriptional regulation; Biological processes; Biological system modeling; Biomedical engineering; Fungi; Gene expression; Genetic algorithms; Humans; Predictive models; Regulators; Simulated annealing;

fLanguage

English

Publisher

ieee

Conference_Titel

Biomedical Engineering and Informatics, 2009. BMEI '09. 2nd International Conference on

Conference_Location

Tianjin

Print_ISBN

978-1-4244-4132-7

Electronic_ISBN

978-1-4244-4134-1

Type

conf

DOI

10.1109/BMEI.2009.5305738

Filename

5305738