Self-organizing neural networks to support the discovery of DNA-binding motifs

Neural Networks

Volumn 19, Issue 6-7, 2006, Pages 950-962

  Mahony, Shaun ^a,b   Benos, Panayiotis V ^a,c   Smith, Terry J ^d   Golden, Aaron ^d  

^a UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^b Learning Research and Development Ctr   (United States)

^c UNIVERSITY OF PITTSBURGH CANCER INSTITUTE   (United States)

^d NATIONAL UNIVERSITY OF IRELAND   (Ireland)

Author keywords

DNA binding motif identification; Self organizing map; Self organizing tree

Indexed keywords

DNA; GENETIC ENGINEERING; LEARNING SYSTEMS; SELF ORGANIZING MAPS; TREES (MATHEMATICS);

BIOINFORMATICS; DNA-BINDING MOTIF IDENTIFICATION; SELF-ORGANIZING TREE;

NEURAL NETWORKS;

DNA;

ALGORITHM; ARTICLE; ARTIFICIAL NEURAL NETWORK; DNA BINDING MOTIF; NONHUMAN; PERFORMANCE; PRIORITY JOURNAL; SCORING SYSTEM; SELF ORGANIZING MAP; TECHNIQUE;

ALGORITHMS; AMINO ACID MOTIFS; ANIMALS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA; HUMANS; MOLECULAR SEQUENCE DATA; NEURAL NETWORKS (COMPUTER); PROTEIN STRUCTURE, TERTIARY; SEQUENCE ANALYSIS, DNA;

EID: 33746710972     PISSN: 08936080     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.neunet.2006.05.023     Document Type: Article

References (52)

1. Abe T., Kanaya S., Kinouchi M., Ichiba Y., Kozuki T., and Ikemura T. A novel bioinformatic strategy for unveiling hidden genome signatures of eukaryotes: Self-organizing map of oligonucleotide frequency. Genome Informatics 13 (2002) 12-20
2. Abe T., Kanaya S., Kinouchi M., Ichiba Y., Kozuki T., and Ikemura T. Informatics for unveiling hidden genome signatures. Genome Research 13 4 (2003) 693-702
3. Aerts S., Van Loo P., Thijs G., Moreau Y., and De Moor B. Computational detection of cis-regulatory modules. Bioinformatics 19 Suppl 2 (2003) II5-II14
4. Aires-de-Sousa J., and Aires-de-Sousa L. Representation of DNA sequences with virtual potentials and their processing by (SEQREP) Kohonen self-organizing maps. Bioinformatics 19 1 (2003) 30-36
5. Arrigo P., Giuliano F., Scalia F., Rapallo A., and Damiani G. Identification of a new motif on nucleic acid sequence data using Kohonen's self-organizing map. Computer Applications in Biosciences 7 3 (1991) 353-357
6. Bailey T.L., and Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings of the International Conference on Intelligent Systems for Molecular Biology 2 (1994) 28-36
7. Bailey T.L., and Elkan C. The value of prior knowledge in discovering motifs with MEME. Proceedings of the International Conference on Intelligent Systems for Molecular Biology 3 (1995) 21-29
8. Barash, Y., Elidan, G., Friedman, N., & Kaplan, T. (2003). Modeling dependencies in protein-DNA binding sites. In Proc. seventh annual inter. conf. on computational molecular biology (RECOMB) (pp. 28-37)
9. Benos P.V., Bulyk M.L., and Stormo G.D. Additivity in protein-DNA interactions: How good an approximation is it?. Nucleic Acids Research 30 20 (2002) 4442-4451
10. Bussemaker H.J., Li H., and Siggia E.D. Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis. Proceedings of the National Academy of Sciences of the United States of America 97 18 (2000) 10096-10100
11. Cartharius K., Frech K., Grote K., Klocke B., Haltmeier M., Klingenhoff A., et al. MatInspector and beyond: Promoter analysis based on transcription factor binding sites. Bioinformatics 21 13 (2005) 2933-2942
12. Day W.H., and McMorris F.R. Critical comparison of consensus methods for molecular sequences. Nucleic Acids Research 20 5 (1992) 1093-1099
13. Dopazo J., and Carazo J.M. Phylogenetic reconstruction using an unsupervised growing neural network that adopts the topology of a phylogenetic tree. Journal of Molecular Evolution 44 2 (1997) 226-233
14. Douzono, H., Hara, S., & Noguchi, Y. (2001). A design method of DNA chips for SNP analysis using self-organizing maps. In Proceedings of the international joint conference on neural networks, 2001
15. Felsenstein J. Maximum-likelihood estimation of evolutionary trees from continuous characters. American Journal of Human Genetics 25 5 (1973) 471-492
16. Fitch W.M. Toward defining the course of evolution: Minimum change for a specified tree topology. Systematic Zoology 20 (1971) 406-416
17. Gorban A.N., Zinovyev A.Y., and Popova T.G. Seven clusters in genomic triplet distributions. In Silico Biology 3 4 (2003) 471-482
18. Gorban, A. N., Zinovyev, A. Y., & Wunsch, D. C. (2003). Application of the method of elastic maps in analysis of genetic texts. In Proceedings of the international joint conference on neural networks, 2003
19. GuhaThakurta D., and Stormo G.D. Identifying target sites for cooperatively binding factors. Bioinformatics 17 7 (2001) 608-621
20. Gupta M., and Liu J.S. Discovery of conserved sequence patterns using a stochastic dictionary model. Journal of the American Statistical Association 98 461 (2003) 55-66
21. Harbison C.T., Gordon D.B., Lee T.I., Rinaldi N.J., Macisaac K.D., Danford T.W., et al. Transcriptional regulatory code of a eukaryotic genome. Nature 431 7004 (2004) 99-104
22. Hayashi H., Abe T., Sakamoto M., Ohara H., Ikemura T., Sakka K., et al. Direct cloning of genes encoding novel xylanases from the human gut. Canadian Journal of Microbiology 51 3 (2005) 251-259
23. Hughes J.D., Estep P.W., Tavazoie S., and Church G.M. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. Journal of Molecular Biology 296 5 (2000) 1205-1214
24. Kanaya S., Kinouchi M., Abe T., Kudo Y., Yamada Y., Nishi T., et al. Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM): Characterization of horizontally transferred genes with emphasis on the E. coli O157 genome. Gene 276 1-2 (2001) 89-99
25. Kohonen T. Self-organizing maps (1995), Springer-Verlag, Berlin
26. Liu X., Brutlag D.L., and Liu J.S. BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pacific Symposium on Biocomputing (2001) 127-138
27. Mahony S., Golden A., Smith T.J., and Benos P.V. Improved detection of DNA motifs using a self-organized clustering of familial binding motifs. Bioinformatics 21 (2005) i283-i291
28. Mahony S., Hendrix D., Golden A., Smith T.J., and Rokhsar D.S. Transcription factor binding site identification using the self-organizing map. Bioinformatics 21 9 (2005) 1807-1814
29. Mahony S., McInerney J.O., Smith T.J., and Golden A. Gene prediction using the Self-Organizing Map: Automatic generation of multiple gene models. BMC Bioinformatics 5 1 (2004) 23
30. Michener C.D., and Sokal R.R. A quantitive approach to a problem in classification. Evolution 11 (1957) 130-162
31. Naenna, T., Bress, R. A., & Embrechts, M. J. (2003). DNA classifications with self-organizing maps (SOMs). In Proceedings of the 2003 IEEE international workshop on soft computing in industrial applications, 2003
32. Oja, M., Sperber, G., Blomberg, J., & Kaski, S. (2004). Grouping and visualizing human endogenous retroviruses by bootstrapping median self-organizing maps. In Proceedings of the 2004 IEEE symposium on computational intelligence in bioinformatics and computational biology, 2004
33. Oja M., Sperber G.O., Blomberg J., and Kaski S. Self-organizing map-based discovery and visualization of human endogenous retroviral sequence groups. International Journal of Neural Systems 15 3 (2005) 163-179
34. Osada R., Zaslavsky E., and Singh M. Comparative analysis of methods for representing and searching for transcription factor binding sites. Bioinformatics 20 18 (2004) 3516-3525
35. Pevzner P.A., and Sze S.H. Combinatorial approaches to finding subtle signals in DNA sequences. Proceedings of the International Conference on Intelligent Systems for Molecular Biology 8 (2000) 269-278
36. Pietrokovski S. Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Acids Research 24 19 (1996) 3836-3845
37. Rigoutsos I., and Floratos A. Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm. Bioinformatics 14 1 (1998) 55-67
38. Roepcke S., Grossmann S., Rahmann S., and Vingron M. T-Reg Comparator: An analysis tool for the comparison of position weight matrices. Nucleic Acids Res 33 Web Server issue (2005) W438-441
39. Saitou N., and Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4 4 (1987) 406-425
40. Sandelin A., Alkema W., Engstrom P., Wasserman W.W., and Lenhard B. JASPAR: An open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Research 32 Database issue (2004) D91-94
41. Sandelin A., and Wasserman W.W. Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics. Journal of Molecular Biology 338 2 (2004) 207-215
42. Schneider T.D., Stormo G.D., Gold L., and Ehrenfeucht A. Information content of binding sites on nucleotide sequences. Journal of Molecular Biology 188 3 (1986) 415-431
43. Schones D.E., Sumazin P., and Zhang M.Q. Similarity of position frequency matrices for transcription factor binding sites. Bioinformatics 21 3 (2005) 307-313
44. Sinha S., and Tompa M. Discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Research 30 24 (2002) 5549-5560
45. Smith T.F., and Waterman M.S. Identification of common molecular subsequences. Journal of Molecular Biology 147 1 (1981) 195-197
46. Wan H., Li L., Federhen S., and Wootton J.C. Discovering simple regions in biological sequences associated with scoring schemes. Journal of Computational Biology 10 2 (2003) 171-185
47. Wang H., Azuaje F., and Black N. Interactive GSOM-based approaches for improving biomedical pattern discovery and visualization. In: Zhang J., He J.-H., and Fu Y. (Eds). Computational and information science: First international symposium, Proceedings Vol. 3314/2004 (2004), Springer-Verlag 556-561
48. Wang H.C., Badger J., Kearney P., and Li M. Analysis of codon usage patterns of bacterial genomes using the self-organizing map. Molecular Biology and Evolution 18 5 (2001) 792-800
49. Wang T., and Stormo G.D. Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics 19 18 (2003) 2369-2380
50. Wingender E., Dietze P., Karas H., and Knuppel R. TRANSFAC: A database on transcription factors and their DNA binding sites. Nucleic Acids Research 24 1 (1996) 238-241
51. Workman C.T., and Stormo G.D. ANN-Spec: A method for discovering transcription factor binding sites with improved specificity. Pacific Symposium on Biocomputing (2000) 467-478
52. Zhao X., Huang H., and Speed T.P. Finding short DNA motifs using permuted Markov models. Journal of Computational Biology 12 6 (2005) 894-906