Quantifying extrinsic noise in gene expression using the maximum entropy framework

Biophysical Journal

Volumn 104, Issue 12, 2013, Pages 2743-2750

  Dixit, Purushottam D ^a  

^a BROOKHAVEN NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI;

BACTERIAL PROTEIN; BACTERIAL RNA; MESSENGER RNA;

BIOLOGICAL MODEL; ENTROPY; ESCHERICHIA COLI; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; PROMOTER REGION;

BACTERIAL PROTEINS; ENTROPY; ESCHERICHIA COLI; MODELS, BIOLOGICAL; PROMOTER REGIONS, GENETIC; RNA, BACTERIAL; RNA, MESSENGER; TRANSCRIPTION, GENETIC;

EID: 84879245436     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2013.05.010     Document Type: Article

References (35)

1. A. Bar-Even, and J. Paulsson N. Barkai Noise in protein expression scales with natural protein abundance Nat. Genet. 38 2006 636 643
2. L. Cai, N. Friedman, and X.S. Xie Stochastic protein expression in individual cells at the single molecule level Nature 440 2006 358 362
3. M.B. Elowitz, and A.J. Levine P.S. Swain Stochastic gene expression in a single cell Science 297 2002 1183 1186
4. B.B. Kaufmann, and A. van Oudenaarden Stochastic gene expression: from single molecules to the proteome Curr. Opin. Genet. Dev. 17 2007 107 112
5. A. Raj, and A. van Oudenaarden Nature, nurture, or chance: stochastic gene expression and its consequences Cell 135 2008 216 226
6. N. Rosenfeld, and J.W. Young M.B. Elowitz Gene regulation at the single-cell level Science 307 2005 1962 1965
7. Y. Taniguchi, and P.J. Choi X.S. Xie Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells Science 329 2010 533 538
8. J.R.S. Newman, and S. Ghaemmaghami J.S. Weissman Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise Nature 441 2006 840 846
9. J. Paulsson Models of stochastic gene expression Phys. Life Rev. 2 2005 157 175
10. A. Raj, and C.S. Peskin S. Tyagi Stochastic mRNA synthesis in mammalian cells PLoS Biol. 4 2006 e309
11. M. Kaern, and T.C. Elston J.J. Collins Stochasticity in gene expression: from theories to phenotypes Nat. Rev. Genet. 6 2005 451 464
12. N. Maheshri, and E.K. O'Shea Living with noisy genes: how cells function reliably with inherent variability in gene expression Annu. Rev. Biophys. Biomol. Struct. 36 2007 413 434
13. H. Maamar, A. Raj, and D. Dubnau Noise in gene expression determines cell fate in Bacillus subtilis Science 317 2007 526 529
14. H.B. Fraser, and A.E. Hirsh M.B. Eisen Noise minimization in eukaryotic gene expression PLoS Biol. 2 2004 e137
15. J. Stewart-Ornstein, J.S. Weissman, and H. El-Samad Cellular noise regulons underlie fluctuations in Saccharomyces cerevisiae Mol. Cell 45 2012 483 493
16. J.R. Chubb, and T. Trcek R.H. Singer Transcriptional pulsing of a developmental gene Curr. Biol. 16 2006 1018 1025
17. I. Golding, and E.C. Cox Eukaryotic transcription: what does it mean for a gene to be 'on'? Curr. Biol. 16 2006 R371 R373
18. L.-H. So, and A. Ghosh I. Golding General properties of transcriptional time series in Escherichia coli Nat. Genet. 43 2011 554 560
19. I. Golding, and J. Paulsson E.C. Cox Real-time kinetics of gene activity in individual bacteria Cell 123 2005 1025 1036
20. P.S. Swain, M.B. Elowitz, and E.D. Siggia Intrinsic and extrinsic contributions to stochasticity in gene expression Proc. Natl. Acad. Sci. USA 99 2002 12795 12800
21. V. Shahrezaei, J. Ollivier, and P. Swain Colored extrinsic fluctuations and stochastic gene expression Mol. Sys. Biol. 4 2008 196
22. M. Thattai, and A. van Oudenaarden Intrinsic noise in gene regulatory networks Proc. Natl. Acad. Sci. USA 98 2001 8614 8619
23. A. Sánchez, and J. Kondev Transcriptional control of noise in gene expression Proc. Natl. Acad. Sci. USA 105 2008 5081 5086
24. M. Hemberg, and M. Barahona Perfect sampling of the master equation for gene regulatory networks Biophys. J. 93 2007 401 410
25. N. Friedman, L. Cai, and X.S. Xie Linking stochastic dynamics to population distribution: an analytical framework of gene expression Phys. Rev. Lett. 97 2006 168302
26. P.D. Dixit A maximum entropy thermodynamics for small systems J. Chem. Phys. 138 2012 184111
27. D. Tjostheim Some doubly stochastic time series models J. Time Ser. Anal. 7 1986 51 72
28. M. Scott, B. Ingalls, and M. Kaern Estimations of intrinsic and extrinsic noise in models of nonlinear genetic networks Chaos 16 2006 026107
29. C.B. Harley, and S. Goldstein Cultured human fibroblasts: distribution of cell generations and a critical limit J. Cell. Physiol. 97 1978 509 516
30. E.T. Jaynes Information theory and statistical mechanics. I Phys. Rev. 106 1957 620 630
31. A. Caticha, and R. Preuss Maximum entropy and Bayesian data analysis: entropic prior distributions Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 70 2004 046127
32. J. Shore, and R. Johnson Axiomatic derivation of the principle of maximum entropy and the principle of minimum cross-entropy IEEE Trans. Inf. Theory 26 1980 26 37
33. G.E. Crooks Beyond Boltzmann-Gibbs statistics: maximum entropy hyperensembles out of equilibrium Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 75 2007 041119
34. R. Reyes-Lamothe, X. Wang, and D. Sherratt Escherichia coli and its chromosome Trends Microbiol. 16 2008 238 245
35. D.T. Gillespie Exact stochastic simulation of coupled chemical reactions J. Phys. Chem. 81 1977 2340 2361