The subclass approach for mutational spectrum analysis: Application of the SEM algorithm

Journal of Theoretical Biology

Volumn 192, Issue 4, 1998, Pages 475-487

  Glazko, Galina B ^a   Milanesi, Luciano ^b   Rogozin, Igor B ^a,b  

^a INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

^b Ist Tecnologie Biomediche A   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ALKYLATING AGENT; MUTAGENIC AGENT;

ALGORITHM; ARTICLE; GENE MUTATION; PRIORITY JOURNAL; STATISTICAL ANALYSIS;

EID: 0032555055     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1006/jtbi.1998.0668     Document Type: Article

References (44)

1. ADAMS, W. T. & SCOPEK, T. R. (1987). Statistical test for the comparison of samples from mutational spectra. J. Mol. Biol. 194, 391-396.
2. BAILEY, T. L. & ELKAN, C. (1995). The value of prior knowledge in discovering motifs with MEME. In: Proceedings Third International Conference on Intelligent Systems for Molecular Biology (Rawlings, C., Clark, D., Altman, R., Hunter, L., Lengauer, T. & Wodak, S., eds), pp. 21-29. Menlo Park: AAAI Press.
3. BEBENEK, K., ABBOTTS, J., ROBERTS, J., WILSON, S. H. & KUNKEL, T. A. (1989). Specificity and mechanism of error-prone replication by human immunodeficiency virus-1 reverse transcriptase. J. Biol. Chem. 264, 16948-16956.
4. BEGNINI, R., PALOMBO, F. & DOGLIOTTI, E. (1992). Multivariate statistical analysis of mutational spectra of alkylating agents. Mutation Res. 267, 77-88.
5. BENZER, S. (1961). On the topology of the genetic fine structure. Proc. Natl. Acad. Sci. U.S.A. 47, 403-415.
6. BOULINKAS, T. (1992). Evolutionary consequences of nonrandom damage and repair of chromatin domains. J. Mol. Evol. 35, 156-180.
7. BROWN, B. W. & LOVATO, J. (1993). Library of C routines for random number generation. Version 1.1.http://lib.stat.cmu.edu.
8. BURNS, P. A., GORDON, A. J. E. & GLICKMAN, B. W. (1987). Influence of neighbouring base sequence on N-methyl-N'-nitro-N-nitrosoguanidine mutagenesis in the lacI gene of Escherichia coli. J. Mol. Biol. 194, 385-390.
9. CARDON, L. R. & STORMO, G. D. (1992). Expectation maximization algorithm for identying protein-binding sites with variable lengths from unaligned DNA fragments. J. Mol. Biol. 223, 159-168.
10. CELEUX, Q. & RIEBOLT, J. (1984). Reconnaissance de melange de densite et classification. Un algorithme d'apprentissage probabiliste: l'algorithme SEM. Rapports de Recerche de 1'INRIA. Centre de Rocquencort.
11. COULONDRE, C., MILLER, J. H., FARABAUGH, P. J. & GILBERT, W. (1978). Molecular basis of base substitution hotspots in Escherichia coli. Nature 274, 775-780.
12. DE BOER, J. G. (1995). Software package for the management of sequencing projects using lacI transgenic animals. Environ. Mol. Mutagen. 25, 256-262.
13. DEMPSTER, A. P., LAIRD, N. M. & RUBIN, D. B. (1977). Maximum likelihood from incomplete data via the EM algorithm (with discussion). J. R. Stat. Soc. Ser. B 39, 1-3.
14. FICKETT, J. W. & GUIGO, R. (1993). Estimation of protein coding density in a corpus of DNA sequence data. Nucleic Acids Res. 21, 2837-2844.
15. FOSTER, P. L., EISENSTADT, E. & CAIRNS, J. (1982). Random components in mutagenesis. Nature 299, 365-367.
16. GORDON, A. J. E., BURNS, P. A., FIX, D. F., YATAGAI, F., ALLEN, F. L., HORSFALL, M. J., et al. (1988a). Missense mutation in the lacI gene of Escherichi coli: inferences of the structure of the represser protein. J. Mol. Biol. 200, 239-251.
17. GORDON, A. J. E., BURNS, P. A. & GLICKMAN, B. W. (1988b). N-methyl-N'-nitro-N-nitrosoguanidine-induced mutation in a RecA strain of Escherichia coli. Mutation Res. 201, 219-228.
18. GORDON, A. J. E., BURNS, P. A. & GLICKMAN, B. W. (1990). N-Methyl-N'-nitro-N-nitrosoguanidine induced DNA sequence alteration: non-random components in alkylation mutagenesis. Mutation Res. 233, 95-103.
19. HAUSER, J., LEVINE, A. S. & K. DIXON, K. (1987). Unique pattern of point mutations arising after gene transfer into mammalian cells. The EMBO J. 6, 63-67.
20. HORSFALL, M. J. & GLICKMAN, B. W. (1988). Mutation site specificity of N-nitroso N-methyl-N-alpha-acetoxybenzyl-amine: a model, derivative of an esophageal carcinogen. Carcinogenesis 9, 1529-1532.
21. HORSFALL, M. J. & GLICKMAN, B. W. (1989). Mutational specificities of environmental carcinogens in lacI gene of Escherichia coli. I - The direct-acting analogue N-nitroso-N-methyl-N-alpha-acetoxymethylamine. Carcinogenesis 10, 817-822.
22. HORSFALL, M. J., ZEILMAKER, M. J., MOHN, G. R. & GLICKMAN, B. W. (1989). Mutational specificities of environmental carciinogens in the lacI gene of Escherichia coli. II - A host-mediated approach to N-nitroso-N, N-dimethylamine and endogenous mutagenesis in vivo. Molecular Carcinogenesis 2, 107-115.
23. HORSFALL, M. J., GORDON, A. J. E., BURNS, P. A., ZIELENSKA, M., VAN DER VLIET, G. M. E. & GLICKMAN, B. W. (1990). Mutational specificity of alkylating agents and the influence of DNA repair. Environ. Mol. Mutagen. 15, 107-122.
24. HUTCHINSON, F. & DONNELAN JR, J. E. (1996). A general database for DNA sequence changes induced by mutagenesis of several bacterial and mammalian genes. Nucleic Acids Res. 24, 172-176.
25. KACHITVICHYANUKUL, V. & SCHMEISER, B. W. (1988). Binomial random variate generation. Commun. ACM 31, 216-223.
26. KUNKEL, T. A. & ALEXANDER, P. S. (1986). The base substitution fidelity of eukaryotic DNA polymerases. Misparing frequencies, site preferences, insertion preferences, and base substitution by dislocation. J. Biol. Chem. 261, 160-166.
27. LAMBERT, I. B., CHIN, T. A., BRYANT, D. W., GORDON, A. J. E., GLICKMAN, B. W. & MCCALLA, D. R. (1991). The mutational specificity of 2-(2-furyl)-3-(5 -nitro-2-furyl)-acrylamide (AF2) in the lacI gene of Escherichia coli. Carcinogenesis 12, 29-34.
28. LAWRENCE, C. E. & REILLY, A. A. (1990). An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins: Structure, Function and Genetics 7, 41-51.
29. LAWRENCE, C. B. & SOLOVYEV, V. V. (1994). Assignment of position-specific error probability to primary DNA sequence data. Nucleic Acids Res. 22, 1272-1280.
30. PIEGORSCH, W. W. & BAILER, A. J. (1994). Statistical approaches for analyzing mutational spectra: some recommendations for categorical data. Genetics 136, 403-416.
31. REDNER, R. A. & WALKER, H. F. (1984). Mixture densities, maximum likelihood and the EM algorithm. SIAM Rev. 26, 195-239.
32. ROGOZIN, I. B. & KOLCHANOV, N. A. (1992). Somatic hypermutagenesis in immunoglobulin genes. II - In uence of neighbouring base sequences on mutagenesis. Biochim. Biophys. Acta 1171, 11-18.
33. ROGOZIN, I. B., SOLOVYEV, V. V. & KOLCHANOV, N. A. (1991). Somatic hypermutagenesis in immunoglobulin genes. I - Correlation between somatic mutations and repeats. Somatic mutation properties and clonal selection. Biochim. Biophys. Acta 1089, 175-182.
34. ROGOZIN, I. B., SREDNEVA, N. E. & KOLCHANOV, N. A. (1992). Intelligent system of mutational analysis. In: Modelling and Computer Methods in Molecular Biology and Genetics (Ratner, V. A. & Kolchanov, N. A., eds), pp. 63-72. New York: Nova Science.
35. ROGOZIN, I. B., SREDNEVA, N. E. & KOLCHANOV, N. A. (1996). Somatic hypermutagenesis in immunoglobulin genes. III -Somatic mutations in the chicken light chain locus. Biochim. Biophys. Acta 1306, 171-178.
36. SANTNER, T. J. & DUFFY, D. E. (1989). The Statistical Analysis of Discrete Data. New York: Springer-Verlag.
37. SCHAAPER, R. M. (1988). Mechanisms of mutagenesis in the Escherichia coli mutator mutD5: role of DNA mismatch repair. Proc Natl. Acad. Sci. U.S.A. 85, 8126-8130.
38. SHLEZINGER, M. I. (1965). On the Spontaneous Image Recognition. Reading Automates. Kiev: Naychnaia Misl' (in Russian).
39. STORMO, G. D., SCHNEIDER, T. D. & GOLD, L. (1986). Quantitative analysis of the relationship between nucleotide sequence and functional activity. Nucleic Acids Res. 14, 6661-6679.
40. 6,-methylguanine mutation and repair is nonuniform. J. Biol. Chem. 261, 9879-9885.
41. TUDDENHAM, E. G. D., COOPER, D. N., GITSCHIER, J. HIGUCHI, M., HOYER, L. W., YOSHIOKA, A., et al. (1991). Haemophilia A: database of nucleotide substitutions, deletions, insertions and rearrangements of the factor VIII gene. Nucleic Acids Res. 19, 4821-4833.
42. WANG, P., PUTERMAN, M. L., COCKBURN, I. & LE, N. (1996). Mixed Poisson regression models with covariate dependent rates. Biometrics 52, 381-400.
43. WOOD, R. D., SKOPEK, T. R. & HUTCHINSON, F. (1984). Changes in DNA base sequence induced by targeted mutagenesis of lambda phage by ultraviolet light. J. Mol. Biol. 173, 273-291.
44. Wu, C. F. J. (1983). On the convergence properties of the EM algorithm. Ann. Statistics 11, 95-103.