Anomaly detection in gene expression via stochastic models of gene regulatory networks

BMC Genomics

Volumn 10, Issue SUPPL. 3, 2009, Pages

  Kim, Haseong ^a   Gelenbe, Erol ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLINE;

ARTICLE; CELL BUDDING; CELL CYCLE; CONTROLLED STUDY; GENE EXPRESSION; GENE REGULATORY NETWORK; GENETIC ALGORITHM; MICROARRAY ANALYSIS; NONHUMAN; SIMULATION; STEADY STATE; STOCHASTIC MODEL; WILD TYPE; YEAST CELL; BIOLOGICAL MODEL; BIOMETRY; CHEMISTRY; CYTOLOGY; GENE EXPRESSION REGULATION; GENETICS; METHODOLOGY; PROBABILITY; SACCHAROMYCETALES; STATISTICS;

SACCHAROMYCETALES;

ANOMALY DETECTION; BIOLOGICAL DATA; CELL CYCLE; DATA SETS; DIFFERENTIALLY EXPRESSED GENE; DISEASE-CAUSING GENE; DYNAMICAL BEHAVIOURS; EXPRESSED GENES; G-NETWORKS; GENE REGULATORY NETWORKS; INFERENCE ALGORITHM; LIVING ORGANISMS; MICROARRAY EXPERIMENTS; REGULATORY GENES; SIMULATION STUDIES; STEADY STATE PROBABILITIES;

BIOINFORMATICS; BIOLOGY; DYNAMICS; GENE EXPRESSION; INFERENCE ENGINES; STOCHASTIC MODELS; STOCHASTIC SYSTEMS;

COMPUTER SIMULATION;

BIOMETRY; CELL CYCLE; GENE EXPRESSION; GENE EXPRESSION REGULATION, FUNGAL; GENE REGULATORY NETWORKS; MODELS, GENETIC; PROBABILITY; SACCHAROMYCETALES; STOCHASTIC PROCESSES;

EID: 71549166029     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-S3-S26     Document Type: Article

References (22)

1. Friedman N, Linial M, Nachman I, Pe'er D. Using Bayesian networks to analyze expression data. Journal of computational biology 2000, 7(3-4):601-620. 10.1089/106652700750050961, 11108481.
2. Schafer J, Strimmer K. An empirical Bayes approach to inferring large-scale gene association networks. Bioinformatics 2005, 21(6):754-764. 10.1093/bioinformatics/bti062, 15479708.
3. Shmulevich I, Gluhovsky I, Hashimoto R, Dougherty E, Zhang W. Steady-state analysis of genetic regulatory networks modelled by probabilistic Boolean networks. Comparative and Functional Genomics 2003, 4(6):601-608. 10.1002/cfg.342, 2447305, 18629023.
4. Ching W, Zhang S, Ng M, Akutsu T. An approximation method for solving the steady-state probability distribution of probabilistic Boolean networks. Bioinformatics 2007, 23(12):1511. 10.1093/bioinformatics/btm142, 17463027.
5. Gelenbe E. Steady-state solution of probabilistic gene regulatory networks. J Theor Biol Phys Rev E 2007, 76:031903.
6. Gelenbe E. Product-form queueing networks with negative and positive customers. Journal of Applied Probability 1991, 656-663.
7. Gelenbe E. G-networks with triggered customer movement. Journal of Applied Probability 1993, 742-748.
8. Arazi A, Ben-Jacob E, Yechiali U. Bridging genetic networks and queueing theory. Physica A: Statistical Mechanics and its Applications 2004, 332:585-616.
9. Gelenbe E, Timotheou S. Random neural networks with synchronized interactions. Neural Computation 2008, 20(9):2308-2324. 10.1162/neco.2008.04-07-509, 18386985.
10. Gillespie D. Exact stochastic simulation of coupled chemical reactions. The journal of physical chemistry 1977, 81(25):2340-2361.
11. Bratsun D, Volfson D, Tsimring L, Hasty J. Delay-induced stochastic oscillations in gene regulation. Proc Natl Acad Sci U S A 2005, 102(41):14593-14598. 10.1073/pnas.0503858102, 16199522, 1253555.
12. Orlando D, Lin C, Bernard A, Wang J, Socolar J, Iversen E, Hartemink A, Haase S. Global control of cell-cycle transcription by coupled CDK and network oscillators. Nature 2008, 453(7197):944-947. 10.1038/nature06955, 2736871, 18463633.
13. McAdams H, Arkin A. Stochastic mechanisms in gene expression. 1997,
14. Paulsson J. Models of stochastic gene expression. Physics of life reviews 2005, 2(2):157-175.
15. Ribeiro A, Zhu R, Kauffman S. A general modeling strategy for gene regulatory networks with stochastic dynamics. Journal of Computational Biology 2006, 13(9):1630-1639. 10.1089/cmb.2006.13.1630, 17147485.
16. Thattai M, van Oudenaarden A. Intrinsic noise in gene regulatory networks. Proc Natl Acad Sci U S A 2001, 98(15):8614-8619. 10.1073/pnas.151588598, 11438714, 37484.
17. Buchler N, Gerland U, Hwa T. Nonlinear protein degradation and the function of genetic circuits. Proc Natl Acad Sci U S A 2005, 102(27):9559-9564. 10.1073/pnas.0409553102, 15972813, 1172234.
18. Goeddel D, Yansura D, Caruthers M. Binding of synthetic lactose operator DNAs to lactose repressors. Proc Natl Acad Sci U S A 1977, 74(8):3292-3296. 10.1073/pnas.74.8.3292, 333432, 431535.
19. Bloom J, Cross F. Multiple levels of cyclin specificity in cell-cycle control. Nature Reviews Molecular Cell Biology 2007, 8(2):149-160. 10.1038/nrm2105, 17245415.
20. Fink G, Spellman P, Sherlock G, Zhang M, Iyer V, Anders K, Eisen M, Brown P, Botstein D, Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular biology of the cell 1998, 9(12):3273-3297. 25624, 9843569.
21. Kim H, Lee J, Park T. Inference of Large Scale Gene Regulatory Networks Using Regressionbased Approach. Journal of Bioinformatics and Computational Biology 2009,
22. Golding I, Paulsson J, Zawilski S, Cox E. Real-time kinetics of gene activity in individual bacteria. Cell 2005, 123(6):1025-1036. 10.1016/j.cell.2005.09.031, 16360033.