Rule extraction from a mutagenicity data set using adaptively grown phylogenetic-like trees

Journal of Chemical Information and Computer Sciences

Volumn 42, Issue 5, 2002, Pages 1104-1111

  Bacha, Patricia A ^a   Gruver, Heather S ^a   Den Hartog, Bobi K ^a   Tamura, Susan Y ^a   Nutt, Ruth F ^a  

^a Bioreason Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PHLOGENETIC-LIKE TREES;

ALGORITHMS; BACTERIA; DATABASE SYSTEMS; DRUG PRODUCTS; OPTIMIZATION; TOXICITY; TREES (MATHEMATICS);

MUTAGENESIS;

MUTAGENIC AGENT;

ALGORITHM; ARTICLE; CHEMICAL MODEL; CHEMISTRY; COMPARATIVE STUDY; FACTUAL DATABASE; HUMAN; MUTAGEN TESTING; PHYLOGENY; STATISTICS; STRUCTURE ACTIVITY RELATION;

ALGORITHMS; DATABASES, FACTUAL; HUMANS; MODELS, CHEMICAL; MUTAGENICITY TESTS; MUTAGENS; PHYLOGENY; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0036708529     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci020366q     Document Type: Article

References (32)

1. International conference on Harmonization: Guidance on specific aspects of regulatory genotoxicity tests for pharmaceuticals. Federal Register 1996, 61 (80), 18197-18202.
2. Ames, B.N.; McCann, H.; Yamasaki, E. Methods for detecting carcinogens and mutagens with the Salmonella/mammalian-microsome mutagenicity test. Mutat. Res. 1975, 31, 347-364.
3. Maron, D.M.; Ames B.N. Revised methods for the Salmonella mutagenicity test. Mutat. Res. 1983, 113, 173-215.
4. Miller, J.A.; Miller, E.C. Ultimate chemical carcinogen as reactive mutagenic electrophiles. In Origin of Human Cancers; Hiatt, H.H., Watson, J.D., Winsten, J.A., Eds.; Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY, 1977; pp 605-627.
5. Ashby, J. Fundamental structural alerts to potential carcinogenicity or noncarcinogenicity. Environ. Mutagen. 1985, 7, 919-921.
6. Ashby, J.; Tennant R.W.; Zeiger, E.; Stasiewiz, S. Classification according to chemical structure, mutagenicity to Salmonella and level of carcinogenicity of a further 42 chemicals tested for carcinogenicity by the U.S. National toxicology Program. Murat. Res. 1989, 223, 73-103.
7. Tennant, R.W.; Ashby, J. Classification according to chemical structure, mutagenicity to Salmonella and level of carcinogenicity of a further 39 chemicals tested for carcinogenicity by the U.S. National Toxicology Program. Mutat. Res. 1991, 257, 209-227.
8. Ashby, J.; Tennant, R.W. Definitive relationships among chemical structure, carcinogenicity and mutagenicity for 301 chemicals tested by the U.S. NTP. Murat. Res. 1991, 257, 229-306.
9. Sanderson, D.M.; Earnshaw, C.G. Computer prediction of possible toxic action from chemical structure; the DEREK system. Human Exp. Toxicol. 1991, 10, 261-273.
10. Woo, Y.-T.; Lai, D.; Argus, M.; Arcos, J. Development of structure-activity relationship rules for predicting carcinogenic potential of chemicals. Toxicol. Lett. 1995, 79, 219-228.
11. Klopman, G. Computer automated structure evaluation of organic molecules. J. Am. Chem. Soc. 1984, 106, 7315-7324.
12. Klopman, G. Multi-Case 1. A hierarchical computer automated structure evaluation program. Quant. Struct. Act. Relat. 1992, 11, 176-184.
13. Enslein, K.; Gombar, V.K.; Blake B.W. Use of SAR in computer-assisted prediction of carcinogenicity and mutagenicity of chemicals by the TOPKAT program. Mutat. Res. 1994, 305, 47-61.
14. Nicolaou, C.; Tamura, S.Y.; Kelley, B.P.; Bassett, S.I.; Nutt, R.F. Analysis of large screening datasets via adaptively grown phylogenic-like trees. J. Chem. Inf. Comput. Sci. 2002, 42, 1069-1079.
15. Bacha, P.; Nutt, R. Development of Chemical-profiling software for early lead selection. Predictive Toxicology; AdvanceTech Monitor: Woburn, MA, 2001; pp 238-250.
16. Rosenkranz, H.; Klopmann, G. Structural alerts to genotoxicity: The interaction of human and artificial intelligence. Mutagenesis 1990, 5, 333-361.
17. Cunningham, A.R.; Rosenkranz, H.S.; Zhang, Y.P.; Klopman G. Indentification of 'genotoxic' and 'nongenotoxic' alerts for cancer in mice: The carcinogenic potency database. Mutat. Res. 1998, 398, 1-17.
18. Greene, N.; Judson, P.N.; Langowski, J.J.; Marchant, C.A. Knowledge-based expert systems for toxicity and metabolism prediction: DEREK, STAR, and METEOR. SAR QSAR Environ. Res. 1999, 10, 299-314.
19. Mersch-Sundermann, V.; Rosenkranz, H.S.; Klopman, G. Structural basis of the genotoxicity of polycyclic aromatic hydrocarbons. Mutagenesis 1992, 7, 211-218.
20. Levin, D.E.; Hollstein, M.; Christman, M.F.; Schwiers, E.A.; Ames B.N.A new Salmonella tester strain (TA102) with A-T base pairs at the site of mutation detects oxidative mutagens. Proc. Natl. Acad. Sci. U.S.A. 1982, 79, 7445-7449.
21. Haworth, S.; Lawlor, T.; Mortelmans, K.; Speck, W.; Zeiger, E. Salmonella Mutagenicity test results for 250 Chemicals. Environ. Mutagen. 1983, 1(Suppl. 1), 3-142.
22. Mortelmans, K.; Haworth, S.; Lawlor, T.; Speck, W.; Tainer, B.; Zeiger, E. Salmonella mutagenicity tests: II. Results from the testing of 270 chemicals. Environ. Mutagen. 1986, 8 (Suppl. 7), 1-119.
23. Zeiger, E.; Anderson, B.; Haworth, S.; Lawlor, T.; Mortelmans, K.; Speck, W. Salmonella mutagenicity tests: III. Results from the testing of 255 chemicals. Environ. Mutagen. 1987, 9 (Suppl. 9), 1-110.
24. Zeiger, E.; Anderson, B.; Haworth, S.; Lawlor, T.; Mortelmans, K. Salmonella mutagenicity tests: IV. Results from the testing of 300 chemicals. Environ. Mutagen. 1988, 11 (Suppl. 12), 1-158.
25. Zeiger, E.; Anderson, B.; Haworth, S.; Lawlor, T.; Mortelmans, K. Salmonella mutagenicity tests: V. Results from the testing of 311 chemicals. Environ. Mutagen. 1992, 19 (Suppl. 2)1, 2-141.
26. Dunkel, V.C.; Zeiger, E.; Brusick, D.; McCoy, E.; McGregor, D.; Mortelmans, K.; Rosenkranz, H.S.; Simmon V.F. Reproducibility of Microbial Mutagenicity Assays: I. Tests with Salmonella typhimurium and Escherichia coli using a standardized protocol. Environ. Mutagen. 1984, 6 (Suppl. 2), 1-254.
27. Dunkel, V.C.; Zeiger, E.; Brusick, D.; McCoy, E.; McGregor, D.; Mortelmans, K.; Rosenkranz, H.S.; Simmon V.F. Reproducibility of Microbial Mutagenicity Assays: II. Testing of carcinogens and noncarcinogens in Salmonella typhimurium and Escherichia coli using a standardized protocol. Environ. Mutagen. 1985, 7 (Suppl. 5), 1-248.
28. LeadPharmer, DrugPharmer, and TreeViewer software from Bioreason, Inc., Santa Fe, NM was used for the analysis. For classification of compounds, the standard multidomain, 3-level method was selected.
29. Zeiger, E.; Margolin, B.H. The proportion of mutagens among chemicals in commerce. Reg. Toxicol. Pharmacol. 2000, 32, 219-225.
30. Rosenkranz, H.S.; Klopman, G. Structural basis of the mutagenicity of phenylazoaniline dyes. Mutation Res. 1989, 221, 217-239.
31. Gibson, G.G.; Skett, P. Introduction to Drug Metabolism, 2nd ed.; Stanley Thornes Publishers Ltd.: Cheltenham, UK, 1999; pp 3, 8, and 10.
32. Chemical Carcinogenesis Research Information System available through TOXNET at http://toxnet.nlm.nih.gov.