On a fundamental structure of gene networks in living cells

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 12, 2012, Pages 4702-4707

  Kravchenko Balasha, Nataly ^a   Levitzki, Alexander ^a   Goldstein, Andrew ^b   Rotter, Varda ^c   Gross, A ^a   Remacle, F ^a,d   Levine, R D ^a,b  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^d UNIVERSITY OF LIÈGE   (Belgium)

Author keywords

Disease patterns; Firmware; Genomics; Surprisal analysis; Thermodynamic analysis

Indexed keywords

ARTICLE; CELL STIMULATION; CELL SURVIVAL; CELL TYPE; COMPUTER PROGRAM; CYTOLOGY; GENE DELETION; GENE EXPRESSION; GENE STRUCTURE; GENETIC VARIABILITY; MOLECULAR STABILITY; PRIORITY JOURNAL; THERMODYNAMICS;

ANIMALS; CELL LINE, TUMOR; COMPUTERS; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; HUMANS; MICE; MODELS, BIOLOGICAL; MODELS, GENETIC; MODELS, STATISTICAL; SOFTWARE; SYSTEMS BIOLOGY; THERMODYNAMICS; TRANSCRIPTION, GENETIC;

EID: 84858695934     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1200790109     Document Type: Article

References (38)

1. de Jonge HJ, et al. (2007) Evidence based selection of housekeeping genes. PLoS ONE 2:e898.
2. Hanahan D, Weinberg RA (2011) Hallmarks of cancer: The next generation. Cell 144:646-674.
3. Alon U (2007) Network motifs: Theory and experimental approaches. Nat Rev Genet 8:450-461.
4. Morris MK, Saez-Rodriguez J, Sorger PK, Lauffenburger DA (2010) Logic-based models for the analysis of cell signaling networks. Biochemistry 49:3216-3224.
5. Davidson E, Levin M (2005) Gene regulatory networks. Proc Natl Acad Sci USA 102:4935.
6. Friedman N, Linial M, Nachman I, Pe'er D (2000) Using Bayesian networks to analyze expression data. J Comput Biol 7:601-620.
7. Koller D, Friedman N (2009) Probabilistic Graphical Models: Principles and Techniques (MIT Press, Cambridge, MA).
8. Lezon TR, Banavar JR, Cieplak M, Maritan A, Fedoroff NV (2006) Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns. Proc Natl Acad Sci USA 103:19033-19038. (Pubitemid 350002823)
9. Margolin AA, et al. (2006) ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 7(Suppl 1):S7.
10. Nykter M, et al. (2008) Critical networks exhibit maximal information diversity in structure-dynamics relationships. Phys Rev Lett 100:058702.
11. Shmulevich I, Aitchison JD (2009) Deterministic and stochastic models of genetic regulatory networks. Methods Enzymol 467:335-356.
12. Amit I, et al. (2009) Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science 326:257-263.
13. Alter O (2007) Genomic signal processing: From matrix algebra to genetic networks. Methods Mol Biol 377:17-60.
14. Bansal M, Belcastro V, Ambesi-Impiombato A, di Bernardo D (2007) How to infer gene networks from expression profiles. Mol Syst Biol 3:78.
15. Bansal M, di Bernardo D (2007) Inference of gene networks from temporal gene expression profiles. IET Syst Biol 1:306-312. (Pubitemid 47354629)
16. Janes KA, Reinhardt HC, Yaffe MB (2008) Cytokine-induced signaling networks prioritize dynamic range over signal strength. Cell 135:343-354.
17. Yeung MKS, Tegnér J, Collins JJ (2002) Reverse engineering gene networks using singular value decomposition and robust regression. Proc Natl Acad Sci USA 99:6163-6168. (Pubitemid 34493283)
18. Huynh-Thu VA, Irrthum A, Wehenkel L, Geurts P (2010) Inferring regulatory networks from expression data using tree-based methods. PLoS ONE 5.
19. Xiao Y, Segal MR (2009) Identification of yeast transcriptional regulation networks using multivariate random forests. PLOS Comput Biol 5:e1000414.
20. Yeger-Lotem E, et al. (2009) Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity. Nat Genet 41:316-323.
21. Omberg L, et al. (2009) Global effects of DNA replication and DNA replication origin activity on eukaryotic gene expression. Mol Syst Biol 5:312.
22. Kravchenko-Balasha N, et al. (2011) Convergence of logic of cellular regulation in different premalignant cells by an information theoretic approach. BMC Syst Biol 5:42.
23. Remacle F, Kravchenko-Balasha N, Levitzki A, Levine RD (2010) Information-theoretic analysis of phenotype changes in early stages of carcinogenesis. Proc Natl Acad Sci USA 107:10324-10329.
24. Macneil LT, Walhout AJ (2011) Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression. Genome Res 21:645-657.
25. Laidler K (1996) A glossary of terms used in chemical kinetics, including reaction dynamics (IUPAC Recommendations 1996). Pure Appl Chem 68:149-192.
26. Levine RD (2005) Molecular Reaction Dynamics (Cambridge Univ Press, Cambridge, UK).
27. Milyavsky M, et al. (2005) Transcriptional programs following genetic alterations in p53, INK4A, and H-Ras genes along defined stages of malignant transformation. Cancer Res 65:4530-4543. (Pubitemid 40740788)
28. Sartor MA, et al. (2010) ConceptGen: A gene set enrichment and gene set relation mapping tool. Bioinformatics 26:456-463.
29. Li CM, Klevecz RR (2006) A rapid genome-scale response of the transcriptional oscillator to perturbation reveals a period-doubling path to phenotypic change. Proc Natl Acad Sci USA 103:16254-16259. (Pubitemid 44715183)
30. Quigley DA, et al. (2011) Network analysis of skin tumor progression identifies a rewired genetic architecture affecting inflammation and tumor susceptibility. Genome Biol 12:R5.
31. Kravchenko-Balasha N, Mizrachy-Schwartz S, Klein S, Levitzki A (2009) Shift from apoptotic to necrotic cell death during human papillomavirus-induced transformation of keratinocytes. J Biol Chem 284:11717-11727.
32. Stickel JS, et al. (2009) HLA ligand profiles of primary renal cell carcinoma maintained in metastases. Cancer Immunol Immunother 58:1407-1417.
33. Ruau D, Ju XS, Zenke M (2006) Genomics of TGF-beta1 signaling in stem cell commitment and dendritic cell development. Cell Immunol 244:116-120. (Pubitemid 46733923)
34. Wang H, Tsai C (2009) Comparison of gene expression profiles between paired primary and metastasis colorectal carcinoma. (GEO database; http://www.ncbi.nlm.nih.gov/geo/).
35. Domka J, Lee J, Bansal T, Wood TK (2007) Temporal gene-expression in Escherichia coli K-12 biofilms. Environ Microbiol 9:332-346. (Pubitemid 46072122)
36. Szklarczyk D, et al. (2011) The STRING database in 2011: Functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 39(Database issue):D561-D568.
37. Batada NN, Hurst LD (2007) Evolution of chromosome organization driven by selection for reduced gene expression noise. Nat Genet 39:945-949. (Pubitemid 47185175)
38. Lehner B (2008) Selection to minimise noise in living systems and its implications for the evolution of gene expression. Mol Syst Biol 4:170.