Statistical model comparison applied to common network motifs

BMC Systems Biology

Volumn 4, Issue , 2010, Pages

  Domedel Puig, Núria ^a   Pournara, Iosifina ^b   Wernisch, Lorenz ^c  

^a UNIVERSITAT POLITÈCNICA DE CATALUNYA   (Spain)

^b UNIVERSITY OF LONDON   (United Kingdom)

^c MRC BIOSTATISTICS UNIT   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI;

ARABINOSE; GALACTOSE;

ALGORITHM; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; BIOLOGY; COMPUTER SIMULATION; ESCHERICHIA COLI; FLAGELLUM; GENETICS; METABOLISM; PROBABILITY; PROTEIN MOTIF; STATISTICAL MODEL; SYSTEMS BIOLOGY; TIME;

ALGORITHMS; AMINO ACID MOTIFS; ARABINOSE; BAYES THEOREM; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; ESCHERICHIA COLI; FLAGELLA; GALACTOSE; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MODELS, STATISTICAL; PROBABILITY; SYSTEMS BIOLOGY; TIME FACTORS;

EID: 77952904483     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-4-18     Document Type: Article

References (31)

1. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA. Transcriptional Regulatory Networks in Saccharomyces cerevisiae. Science 2002, 298(5594):799-804. 10.1126/science.1075090, 12399584.
2. Shen-Orr SS, Milo R, Mangan S, Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nature Genetics 2002, 31:64-68. 10.1038/ng881, 11967538.
3. Alon U. An introduction to Systems Biology. Design principles of biological circuits 2007, Chapman & Hall/CRC Mathematical & Computational Biology.
4. Tyson JJ, Chen KC, Novak B. Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Current Opinion in Cell Biology 2003, 15(2):221-231. 10.1016/S0955-0674(03)00017-6, 12648679.
5. Mangan S, Zaslaver A, Alon U. The Coherent Feedforward Loop Serves as a Sign-sensitive Delay Element in Transcription Networks. Journal of Molecular Biology 2003, 334(2):197-204. 10.1016/j.jmb.2003.09.049, 14607112.
6. Kalir S, Mangan S, Alon U. A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli. Molecular Systems Biology 2005, 1. 2005.0006, 10.1038/msb4100010, 1681456, 16729041.
7. Mangan S, Itzkovitz S, Zaslaver A, Alon U. The Incoherent Feed-forward Loop Accelerates the Response-time of the gal System of Escherichia coli. Journal of Molecular Biology 2006, 356(5):1073-1081. 10.1016/j.jmb.2005.12.003, 16406067.
8. Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette M, Alon U. A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nature Methods 2006, 3(8):623-628. 10.1038/nmeth895, 16862137.
9. Cohen AA, Geva-Zatorsky N, Eden E, Frenkel-Morgenstern M, Issaeva I, Sigal A, Milo R, Cohen-Saidon C, Liron Y, Kam Z, Cohen L, Danon T, Perzov N, Alon U. Dynamic proteomics of individual cancer cells in response to a drug. Science 2008, 322(5907):1511-1516. 10.1126/science.1160165, 19023046.
10. Segal E, Barash Y, Simon I, Friedman N, Koller D. From promoter sequence to expression: a probabilistic framework. Proceedings of the Sixth Annual International Conference on Computational Molecular Biology (RECOMB) 2002,
11. Brazhnik P, de la Fuente A, Mendes P. Gene networks: how to put the function in genomics. TRENDS in Biotechnology 2002, 20(11):467-472. 10.1016/S0167-7799(02)02053-X, 12413821.
12. Cavalier G, Anastassiou D. Phenotype analysis using network motifs derived from changes in regulatory network dynamics. Proteins: Structure, Function and Bioinformatics 2005, 60(3):525-546.
13. Swameye I, Müller TG, Timmer J, Sandra O, Klingmüller U. Identification of nucleocytoplasmic cycling as a remote sensor in cellular signaling by databased modeling. PNAS 2003, 100(3):1028-1033. 10.1073/pnas.0237333100, 298720, 12552139.
14. Vyshemirsky V, Girolami MA. Bayesian ranking of biochemical system models. Bioinformatics 2008, 24(6):833-839. 10.1093/bioinformatics/btm607, 18057018.
15. Gelman A, Carlin JB, Stern HS, Rubin DB. Bayesian data analysis 2004, Chapman & Hall/CRC Texts in Statistical Science.
16. Gilks WR, Richardson S, Spiegelhalter DJ. Markov Chain Monte Carlo in Practice 1996, Chapman & Hall/CRC Interdisciplinary Statistics Series.
17. Gelfand AE, Dey DK. Bayesian model choice: asymptotic and exact calculations. Journal of the Royal Statistics Society Series B (Methodological) 1994, 56(3):501-514.
18. Miazhynskaia T, Dorffner G. A comparison of Bayesian model selection based on MCMC with an application to GARCH-type models. Statistical Papers 2006, 47:525-549.
19. Spiegelhalter DJ, Best NG, Carlin BP, Linde A. Bayesian measures of model complexity and fit. Journal of the Royal Statistics Society Series B 2002, 64(4):583-639.
20. Ripley BD. Pattern Recognition and Neural Networks 1996, Cambridge University Press.
21. Kass RE, Raftery AE. Bayes Factors. Journal of the American Statistical Association 1995, 90(430):773-795.
22. Burnham KP, Anderson DR. Model Selection and Multimodel Inference: a Practical Information-Theoretic Approach 2002, New York: Springer-Verlag, 2.
23. Bois FY, Maszle DR. MCSim: A Monte Carlo Simulation Program. Journal of Statistical Software 1997, 2(9):1-60.
24. The R Project for Statistical Computing. , http://www.R-project.org
25. Ronen M, Rosenberg R, Shraiman BI, Alon U. Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics. Proceedings of the National Academy of Sciences of the USA 2002, 99(16):10555-10560. 10.1073/pnas.152046799, 124972, 12145321.
26. Alon U. Network motifs: theory and experimental approaches. Nature Reviews Genetics 2007, 8(6):450-461. 10.1038/nrg2102, 17510665.
27. Batchelor E, Loewer A, Lahav G. The ups and downs of p53: understanding protein dynamics in single cells. Nature Reviews Cancer 2009, 9(5):371-377. 10.1038/nrc2604, 19360021.
28. Mangan S, Alon U. Structure and function of the feed-forward loop network motif. Proceedings of the National Academy of Sciences of the USA 2003, 100(21):11980-11985. 10.1073/pnas.2133841100, 218699, 14530388.
29. Ma HW, Kumar B, Ditges U, Gunzer F, Buer J, Zeng AP. An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. Nucleic Acids Research 2004, 32(22):6643-6649. 10.1093/nar/gkh1009, 545451, 15604458.
30. Kalir S, Alon U. Using a quantitative blueprint to reprogram the dynamics of the flagella gene network. Cell 2004, 117(6):713-720. 10.1016/j.cell.2004.05.010, 15186773.
31. Omlin M, Reichert P. A comparison of techniques for the estimation of model prediction uncertainty. Ecological Modelling 1999, 115:45-59.