Maximal entropy inference of oncogenicity from phosphorylation signaling

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

Volumn 107, Issue 13, 2010, Pages 6112-6117

  Graeber, T G ^a   Heath, J R ^a,b   Skaggs, B J ^a   Phelps, M E ^a   Remacle, F ^a,c   Levine, R D ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^c UNIVERSITY OF LIÈGE   (Belgium)

Author keywords

High throughput measurements; Information theory; Phospho proteomics; Signal transduction networks; Systems biology

Indexed keywords

BCR ABL PROTEIN; PHOSPHOTRANSFERASE INHIBITOR;

ARTICLE; CARCINOGENICITY; CONTROLLED STUDY; ENTROPY; HIGH THROUGHPUT SCREENING; INFORMATION SCIENCE; LEUKEMIA; PHENOTYPE; POINT MUTATION; PREDICTION; PRIORITY JOURNAL; PROTEIN PHOSPHORYLATION; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

AMINO ACID SEQUENCE; ENTROPY; FUSION PROTEINS, BCR-ABL; GENES, ABL; HUMANS; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE DATA; ONCOGENES; PHENOTYPE; PHOSPHORYLATION; POINT MUTATION; PROTEIN STRUCTURE, TERTIARY; PROTEIN-TYROSINE KINASES; PROTEOMICS; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

EID: 77950529261     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1001149107     Document Type: Article

References (30)

1. Hunter T (1998) The Croonian Lecture 1997. The phosphorylation of proteins on tyrosine: its role in cell growth and disease. Philos Trans R Soc Lond B Biol Sci 353: 583-605.
2. Irish JM, et al. (2004) Single cell profiling of potentiated phospho-protein networks in cancer cells. Cell 118:217-228. (Pubitemid 38962577)
3. Rikova K, et al. (2007) Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell 131:1190-1203. (Pubitemid 350235027)
4. Janes KA, et al. (2005) A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis. Science 310:1646-1653.
5. Skaggs BJ, et al. (2006) Phosphorylation of the ATP-binding loop directs oncogenicity of drug-resistant BCR-ABL mutants. Proc Natl Acad Sci USA 103:19466-19471.
6. Jaynes ET (2004) Probability Theory: The Logic of Science (Cambridge Univ Press, Cambridge).
7. Gibbs JW (1961) The Scientific Papers of J. W. Gibbs (Dover, New York).
8. Mayer JE, Mayer MG (1966) Statistical mechanics (Wiley, New York).
9. Ivakhno S, Armstrong JD (2007) Non-linear dimensionality reduction of signaling networks. BMC Syst Biol 1:27. (Pubitemid 47162441)
10. Janes KA, Lauffenburger DA (2006) A biological approach to computational models of proteomic networks. Curr Opin Chem Biol 10:73-80. (Pubitemid 43202291)
11. Krawitz P, Shmulevich I (2007) Entropy of complex relevant components of Boolean networks. Phys Rev E Stat Nonlin Soft Matter Phys 76:036115. (Pubitemid 47510099)
12. 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)
13. 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.
14. Nykter M, et al. (2008) Critical networks exhibit maximal information diversity in structure-dynamics relationships. Phys Rev Lett 100:058702.
15. Rosvall M, Bergstrom CT (2007) An information-theoretic framework for resolving community structure in complex networks. Proc Natl Acad Sci USA 104:7327-7331. (Pubitemid 47185904)
16. Slonim N, Atwal GS, Tkacik G, Bialek W (2005) Information-based clustering. Proc Natl Acad Sci USA 102:18297-18302.
17. Tkacik G, Callan CG, Jr, Bialek W (2008) Information flow and optimization in transcriptional regulation. Proc Natl Acad Sci USA 105:12265-12270.
18. Ziv E, Nemenman I, Wiggins CH (2007) Optimal signal processing in small stochastic biochemical networks. PLoS One 2:e1077.
19. Callen HB (1985) Thermodynamics and an Introduction to Thermostatics (Wiley, NY).
20. Janes KA, et al. (2004) Cue-signal-response analysis of TNF-induced apoptosis by partial least squares regression of dynamic multivariate data. J Comput Biol 11: 544-561.
21. Picard RR, Cook RD (1997) Cross-Validation of Regression Models. J Am Stat Assoc 79:575-583.
22. Gorre ME, et al. (2001) Clinical resistance to STI-571 cancer therapy caused by BCR-ABL gene mutation or amplification. Science 293:876-880.
23. Kinsey JL, Levine RD (1979) A Performance Criterion for Information Theoretic Data Analysis. Chem Phys Lett 65:413-416.
24. Remacle F, Levine RD (2009) The elimination of redundant constraints in surprisal analysis of unimolecular dissociation and other endothermic processes. J Phys Chem A 113:4658-4664.
25. van den Berg RA, Hoefsloot HC, Westerhuis JA, Smilde AK, van der Werf MJ (2006) Centering, scaling, and transformations: improving the biological information content of metabolomics data. BMC Genomics 7:142.
26. Bar-Even A, et al. (2006) Noise in protein expression scales with natural protein abundance. Nat Genet 38:636-643. (Pubitemid 43927304)
27. Bernstein RB, Levine RD (1972) Entropy and Chemical Change. 1. Characterization of Product (and Reactant) Energy Distributions in Reactive Molecular Collisions: Information and Entropy Deficiency. J Chem Phys 57:434-449.
28. Dinur U, Levine RD (1975) On the entropy of a continuous distribution. Chem Phys 9: 17-27.
29. Ahmed NA, Gokhale DV (1989) Entropy expressions and their estimators for multivariate distributions. IEEE Trans Inf Theory 35:688-692.
30. Ash RB (1990) Information Theory (Dover, Mineola, NY).