Study of proteome maps using partial ordering

Journal of Theoretical Biology

Volumn 266, Issue 1, 2010, Pages 21-28

  Randić, Milan ^a   Novič, Marjana ^a   Vračko, Marjan ^a   Plavšić, Dejan ^b  

^a NATIONAL INSTITUTE OF CHEMISTRY   (Slovenia)

^b RUDER BO KOVI INSTITUTE   (Croatia)

Author keywords

Partial ordering; Peroxisome; Proliferators; Proteomics maps

Indexed keywords

CLOFIBRATE; PERFLUORODECANOIC ACID; PERFLUOROOCTANOIC ACID; PEROXISOME PROLIFERATOR; PHTHALIC ACID BIS(2 ETHYLHEXYL) ESTER;

EIGENVALUE; MAP; PROTEIN; RODENT;

ARTICLE; LIVER CELL; MATHEMATICAL COMPUTING; MATHEMATICS; NONHUMAN; PARTIAL ORDERING; PEPTIDE MAPPING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; QUANTITATIVE ANALYSIS;

RATTUS;

EID: 77953934649     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2010.06.008     Document Type: Article

References (44)

1. Anderson N.L., Esquer-Blasco R., Richardson F., Foxworthy P., Eacho P. The effect of peroxisome proliferators on protein abundances in mouse liver. Toxicol. Appl. Pharmacol. 1996, 137:75-89.
2. Basak S.C., Gute B.D., Grunwald G.D. A hierarchical approach to the development of QSAR models using topological, geometrical, and quantum chemical parameters. Topological Indices and Related Descriptors. QSAR and QSPR 1999, 675-696. Gordon and Breach Science Publishers, The Netherlands. J. Devillers, A.T. Balaban (Eds.).
3. Basak S.C., Grunwald G.D. Use of topological space and property space in selecting structural analogous. Math. Modelling Sci. Comput. 1994, 4:464-469.
4. Basak S.C., Grunwald G.D., Host G.E., Niemi G.J., Bradbury S.P. A comparative study of molecular similarity, statistical, and neural network methods for modes of action of chemicals. Environ. Toxicol. Chem. 1998, 17:1056-1064.
5. Basak S.C., Magnusaon V.R., Niemi G.J., Regal R.R. Determining structural similarity of chemicals using graph-theoretic indices. Discrete Appl. Math. 1988, 19:17-44.
6. Basak S.C., Mills D., Gute B.D., Grunwald G.D., Balaban A.T. Applications of topological indices in property/bioactivity/toxicity prediction of chemicals. Topology in Chemistry: Discrete Mathematics of Molecules 2002, 113-184. Horwood, Chichester, UK. D.H. Rouvray, R.B. King (Eds.).
7. Calabrese E.J., Baldwin L.A. Toxicology rethinks its central belief. Nature 2003, 412:691-692.
8. Gute B.D., Basak S.C. Molecular similarity-based estimation of properties: a comparison of three structure spaces. J. Mol. Graphics 2001, 20:95-109.
9. Harary F. Graph Theory 1969, Addison-Wesley, Reading, MA.
10. Hardy G.H., Littlewood J.E., Pólya G. Inequalities 1988, Cambridge University Press, Cambridge, England. second ed.
11. Klein, D. J.; Brickmann (guest editors). Partial Orderings in Chemistry, MATCH (Mathematical Chemistry Communication), 2000, No. 42.
12. Kowalski B.R., Bender C.F. A powerful approach to interpreting chemical data. J. Am. Chem. Soc. 1972, 94:5632-5639.
13. Lovász L., Pelikán, J J. On the eigenvalues of trees. Period. Math. Hung 1973, 3:175-182.
14. MATLAB (abbreviation for Matrix Laboratory) is a product of The MathWorks, Inc., 3 Apple Hill Drive, Natick, MA, 01760.
15. Muirhead R.F. Some methods applicable to identities and inequalities of symmetric algebraic functions of n letters. Proc. Edinburgh Math. Soc. 1903, 21:144-157. [R. F. Muirhead (1860-1941)].
16. Randić M. Design of molecules with desired properties. Molecular similarity approach to property optimization. Concepts and Applications of Molecular Similarity 1990, 77-145. Wiley, New York. M.A. Johnson, G. Maggiora (Eds.).
17. Randić M. Novel graph theoretical approach to heteroatom in quantitative structure-activity relationships. Chemometrics Intel. Lab. Syst. 1991, 10:213-227.
18. Randić M. On computation of optimal parameters for multivariate analysis of structure-property relationship. J. Comput. Chem. 1991, 12:970-980.
19. Randić M. Similarity methods of interest in chemistry. Mathematical Methods in Contemporary Chemistry 1996, Gordon & Breach Publications, Inc., New York. S. Kuchanov (Ed.).
20. Randić M. On structural ordering and branching of acyclic saturated hydrocarbons. J. Math. Chem. 1998, 24:345-358.
21. Randić M. On characterization of pharmacophore. Acta Chim. Slovenica 2000, 47:143-151.
22. Randić M. On graphical representation of proteomics and their numerical characterization. J. Chem. Inf. Comput. Sci. 2001, 41:1330-1338.
23. Randić M. A graph theoretical characterization of proteomics maps. Int. J. Quantum Chem. 2002, 90:848-858.
24. Randić M. Quantitative characterization of proteome: dependence on the number of proteins considered. J. Proteome Res. 2006, 5:1575-1579.
25. Randić M., Basak S.C. A comparative study of proteomics maps using graph theoretical biodescriptors. J. Chem. Inf. Comput. Sci. 2002, 42:983-993.
26. Randić M., Basak S.C. On similarity of proteome maps. Med. Chem. Res. 2004, 13:800-811.
27. Randić M., Basak S.C., Plavšić D. Novel graphical matrix and distance-based molecular descriptors. Croat. Chem. Acta 2004, 77:251-257.
28. Randić M., Dobrowolski J.Cz. Optimal molecular connectivity descriptors for nitrogen-containing molecules. Int. J. Quantum Chem. 1998, 70:1209-1215.
29. Randić M., Estrada E. Order from chaos: observing hormesis at the proteome level. J. Proteome Res. 2005, 4:2133-2136.
30. Randić M., Guo X., Bobst S. Use of path matrices for characterization of molecular structure. DIMACS Series in Disc. Math. Theor. Comput. Sci. 2000, 51:305-322.
31. Randić M., Jerman-Blažič B., Rouvray D.H., Seybold P.G., Grossman S.C. The search for active substructure in structure-activity studies. Int. J. Quantum Chem.: Quantum Biol. Symp. 1987, 14:245-260.
32. Randić M., Kleiner A.F., De Alba L.M. Distance/distance matrices. J. Chem. Inf. Comput. Sci. 1994, 34:277-286.
33. Randić, M., Lerš, N., Vukučević, D., Plavšić, D., Gute, B.D., Basak, S.C., 2005.Canonical labeling of proteome maps. J. Proteome Res. 4, 1347-1352.
34. Randić M., Mills D., Basak.S.C. On use of variable connectivity index for characterization of amino acids. Int. J. Quantum Chem. 2000, 80:1199.
35. Randić M., Novič M., Vračko M. On characterization of dose variations of 2-D proteomics maps by matrix invariants. J. Proteome Res. 2002, 1:217-226.
36. Randić, M., Orel R. On numerical characterization of proteomics maps based on partitioning of 2-D maps into Voronoi regions. J. Math. Chem., submitted for publication.
37. Randić, M., Plavšić D., in preparation.
38. Randić M., Plavšić D., Razinger M. Double invariants. MATCH - Commun. Math. Comput. Chem. 1997, 35:243-259.
39. Randić M., Vračko M., Novič M. Eigenvalues as molecular descriptors. QSPR/QSAR Studies by Molecular Descriptors 2001, 147-211. Nova Science Publishers, Huntington, NY. M.V. Diudea (Ed.).
40. Randić M., Wilkins C.L. Graph theoretical ordering of structures as a basis for systematic searches for regularities in molecular data. J. Phys. Chem. 1979, 83:1525-1540.
41. Randić M., Wilkins C.L. On a graph theoretical basis for ordering of structures. Chem. Phys. Lett. 1979, 63:332-336.
42. Randić M., Witzmann F., Vračko M., Basak S.C. On characterization of proteomics maps and chemically induced changes in proteome using matrix invariants: application to peroxisome proliferators. Med. Chem. Rev. 2001, 10:456-479.
43. Randić M., Witzmann F.A., Kodali V., Basak S.C. Dependence of a characterization of proteomics maps on the number of protein spots considered. J. Chem. Inf. Model. 2006, 46:116-122.
44. Randić M., Zupan J., Novič M. On 3-D graphical representation of proteomics maps. Chem. Inf. Comput. Sci. 2001, 41:1334-1339.