Prediction of transcriptional regulation by analysis of the non-coding genome

Current Genomics

Volumn 4, Issue 3, 2003, Pages 217-224

  van Helden, Jacques ^a  

^a UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

Author keywords

Bioinformatics; Comparative genomics; Pattern discovery; Sequence analysis; Transcriptional regulation

Indexed keywords

GENE PRODUCT;

ALGORITHM; AMINO ACID SEQUENCE; CELL CYCLE; COMPARATIVE GENE MAPPING; COMPUTER ANALYSIS; EMBRYO DEVELOPMENT; GENE FUNCTION; GENE INTERACTION; GENE SEQUENCE; GENETIC CODE; GENOME ANALYSIS; HUMAN; IMMUNE RESPONSE; METABOLIC REGULATION; NONHUMAN; OPEN READING FRAME; PREDICTION; REVIEW; SEQUENCE ANALYSIS; TRANSCRIPTION REGULATION;

EID: 0037377452     PISSN: 13892029     EISSN: None     Source Type: Journal    
DOI: 10.2174/1389202033490448     Document Type: Review

References (47)

1. van Helden, J., Andre, B. and Collado-Vides, J. A web site for the computational analysis of yeast regulatory sequences. Yeast, 2000, 16: 177-87.
2. Hertz, G. Z. and Stormo, G. D. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 1999, 15: 563-77.
3. Hertz, G. Z., Hartzell, G. W. D. and Stormo, G. D. Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Comput. Appl. Biosci. 1990, 6: 81-92.
4. Wolfertstetter, F., Frech, K., Herrmann, G. and Werner, T. Identification of functional elements in unaligned nucleic acid sequences by a novel tuple search algorithm. Comput. Appl. Biosci. 1996, 12: 71-80.
5. van Helden, J., Andre, B. and Collado-Vides, J. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol. 1998, 281: 827-42.
6. Brazma, A., Jonassen, I., Vilo, J. and Ukkonen, E. Predicting gene regulatory elements in silico on a genomic scale. Genome. Res. 1998, 8: 1202-15.
7. Bussemaker, H. J., Li, H. and Siggia, E. D. Regulatory element detection using a probabilistic segmentation model. Ismb. 2000, 8: 67-74.
8. Bussemaker, H. J., Li, H. and Siggia, E. D. From the cover: building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis. Proc. Natl. Acad. Sci. U.S.A. 2000, 97: 10096-100.
9. Vanet, A., Marsan, L. and Sagot, M. F. Promoter sequences and algorithmical methods for identifying them. Res. Microbiol. 1999, 150: 779-99.
10. van Helden, J., Rios, A. F. and Collado-Vides, J. Discovering regulatory elements in non-coding sequences by analysis of spaced dyads. Nucleic Acids Res. 2000, 28: 1808-18.
11. Mengeritsky, C. and Smith, T. F. Recognition of characteristic patterns in sets of functionally equivalent DNA sequences. Comput. Appl. Biosci. 1987, 3: 223-227.
12. van Helden, J., del Olmo, M. and Perez-Ortin, J. E. Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals. Nucleic Acids Res. 2000, 28: 1000-10.
13. van Helden, J., Gilbert, D., Wernisch, L., Schroeder, M. and Wodak, S. Applications of regulatory sequence analysis and metabolic network analysis to the interpretation of gene expression data. Lecture Notes in Computer Sciences, 2001, 2066: 155-172.
14. Stormo, G. D. and Hartzell, G. W. D. Identifying protein-binding sites from unaligned DNA fragments. Proc. Natl. Acad. Sci. U.S.A. 1989, 86: 1183-7.
15. Lawrence, C. E., Altschul, S. F., Boguski, M. S., Liu, J. S., Neuwald, A. F. and Wootton, J. C. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 1993, 262: 208-14.
16. Neuwald, A. F., Liu, J. S. and Lawrence, C. E. Gibbs motif sampling: detection of bacterial outer membrane protein repeats. Protein Sci. 1995, 4: 1618-32.
17. Roth, F. P., Hughes, J. D., Estep, P. W. and Church, G. M. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat. Biotechnol. 1998, 16: 939-45.
18. Frech, K., Quandt, K. and Werner, T. Software for the analysis of DNA sequence elements of transcription. Comput. Appl. Biosci. 1997, 13: 89-97.
19. 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. J. Mol. Biol. 2000, 296: 1205-14.
20. McGuire, A. M., Hughes, J. D. and Church, G. M. Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. Genome. Res. 2000, 10: 744-57.
21. Blattner, F. R., Plunkett, G., 3rd, Bloch, C. A., Perna, N. T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C. K., Mayhew, G. F., Gregor, J., Davis, N. W., Kirkpatrick, H. A., Goeden, M. A., Rose, D. J., Mau, B. and Shao, Y. The complete genome sequence of Escherichia coli K-12. Science, 1997, 277: 1453-74.
22. Thieffry, D., Salgado, H., Huerta, A. M. and Collado-Vides, J. Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12. Bioinformatics, 1998, 14: 391-400.
23. Fondrat, C. and Kalogeropoulos, A. Approaching the function of new genes by detection of their potential upstream activation sequences in Saccharomyces cerevisiae: application to chromosome III. Current Genetics, 1994, 25: 396-406.
24. Zhu, J. and Zhang, M. Q. SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics, 1999, 15: 607-11.
25. DeRisi, J. L., Iyer, V. R. and Brown, P. O. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science, 1997, 278: 680-6.
26. Brown, P. O. and Botstein, D. Exploring the new world of the genome with DNA microarrays. Nat. Genet. 1999, 21: 33-7.
27. Tavazoie, S., Hughes, J. D., Campbell, M. J., Cho, R. J. and Church, G. M. Systematic determination of genetic network architecture. Nat. Genet. 1999, 22: 281-5.
28. Vilo, J., Brazma, A., Jonassen, I. and Ukkonen, E. Mining for Putative Regulatory Elements in the Yeast Genome Using Gene Expression Data. ISMB, 2000.
29. Eisen, M. B., Spellman, P. T., Brown, P. O. and Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. U.S.A. 1998, 95: 14863-8.
30. Tamayo, P., Slonim, D., Mesirov, J., Zhu, Q., Kitareewan, S., Dmitrovsky, E., Lander, E. S. and Golub, T. R. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc. Natl. Acad. Sci. U.S.A. 1999, 96: 2907-12.
31. Brown, M. P., Grundy, W. N., Lin, D., Cristianini, N., Sugnet, C. W., Furey, T. S., Ares, M. and Haussler, D. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc. Natl. Acad. Sci. U.S.A. 2000, 97: 262-7.
32. Sharan, R. and Shamir, R. CLICK: a clustering algorithm with applications to gene expression analysis. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2000, 8: 307-16.
33. Bussemaker, H. J., Li, H. and Siggia, E. D. Regulatory element detection using correlation with expression. Nat. Genet. 2001, 27: 167-71.
34. Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G. D. and Maltsev, N. The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. USA 1999, 96(6): 2896-901.
35. Marcotte, E. M., Pellegrini, M., Ng, H. L., Rice, D. W., Yeates, T. O. and Eisenberg, D. Detecting protein function and protein-protein interactions from genome sequences. Science, 1999, 285: 751-3.
36. Marcotte, E. M., Pellegrini, M., Thompson, M. J., Yeates, T. O. and Eisenberg, D. A combined algorithm for genome-wide prediction of protein function. Nature, 1999, 402: 83-6.
37. Enright, A. J., Iliopoulos, I., Kyrpides, N. C. and Ouzounis, C. A. Protein interaction maps for complete genomes based on gene fusion events. Nature, 1999, 402: 86-90.
38. Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D. and Yeates, T. O. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. U.S.A. 1999, 96: 4285-8.
39. Wasserman, W. W. and Fickett, J. W. Identification of regulatory regions which confer muscle-specific gene expression. J. Mol. Biol. 1998, 278: 167-81.
40. Wasserman, W. W., Palumbo, M., Thompson, W., Fickett, J. W. and Lawrence, C. E. Human-mouse genome comparisons to locate regulatory sites [In Process Citation]. Nat. Genet. 2000, 26: 225-8.
41. Fickett, J. W. and Wasserman, W. W. Discovery and modeling of transcriptional regulatory regions. Curr. Opin. Biotechnol. 2000, 11: 19-24.
42. McCue, L., Thompson, W., Carmack, C., Ryan, M. P., Liu, J. S., Derbyshire, V. and Lawrence, C. E. Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res. 2001, 29: 774-82.
43. Salgado, H., Santos-Zavaleta, A., Gama-Castro, S., Millan-Zarate, D., Diaz-Peredo, E., Sanchez-Solano, F., Perez-Rueda, E., Bonavides-Martinez, C. and Collado-Vides, J. RegulonDB (version 3.2): transcriptional regulation and operon organization in escherichia coli K-12 [In Process Citation]. Nucleic Acids Res. 2001, 29: 72-4.
44. Huerta, A. M., Salgado, H., Thieffry, D. and Collado-Vides, J. RegulonDB: a database on transcriptional regulation in Escherichia coli. Nucleic Acids Res. 1998, 26: 55-9.
45. Robison, K., McGuire, A. M. and Church, G. M. A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J. Mol. Biol. 1998, 284: 241-54.
46. Mironov, A. A., Koonin, E. V., Roytberg, M. A. and Gelfand, M. S. Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes. Nucleic Acids Res. 1999, 27: 2981-9.
47. Gelfand, M. S., Pavel, S., Novihkov, E. S. and Mironov, A. A. Comparative analysis of regulatory patterns in bacterial genomes. Briefings in Bioinformatics, 2000, 1: 357-371.