Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies

Journal of Molecular Biology

Volumn 281, Issue 5, 1998, Pages 827-842

  Van Helden, J ^a   Andre B ^b   Collado Vides, J ^a  

^a Ctro Invest Sobre Fijacion N   (Mexico)

^b Bd du Triomphe B 1050   (Belgium)

Author keywords

Computational methods; DNA microarray technology; Functional genomics; Transcriptional regulation; Yeast

Indexed keywords

FUNGAL DNA; OLIGONUCLEOTIDE;

ALGORITHM; ARTICLE; BINDING SITE; DNA BINDING; GENE EXPRESSION REGULATION; GENE FREQUENCY; NONHUMAN; PRIORITY JOURNAL; REGULATOR GENE; SACCHAROMYCES CEREVISIAE; TECHNIQUE;

SACCHAROMYCES CEREVISIAE;

EID: 0032483307     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1947     Document Type: Article

References (45)

1. Balzi E., Goffeau A. Yeast multidrug resistance the PDR network. J. Bioenerget. Biomembr. 27:1995;71-76
2. Blaiseau P.-L., Isnard A.-D., Surdin-Kerjan Y., Thomas D. Met31p and Met32p, two related zinc finger proteins, are involved in transcriptional regulation of yeast sulfur amino acid metabolism genes. Mol. Cell. Biol. 17:1997;3640-3648
3. Bodnar J.W., Ward D.C. Highly recurring sequence elements identified in eukaryotic DNAs by computer analysis are often homologous to regulatory sequences or protein binding sites. Nucl. Acids Res. 14:1987;1835-1851
4. Bysani N., Daugherty J.R., Cooper T.G. Saturation mutagenesis of the UASNTR (GATAA) responsible for nitrogen catabolite repression-sensitive transcriptional activation of the allantoin pathway genes in Saccharomyces cerevisiae. J. Bacteriol. 173:1991;4977-4982
5. Cardon L.R., Stormo G.D. Expectation maximisation algorithm for identifying protein-binding sites with variable lengths from unaligned DNA fragments. J. Mol. Biol. 223:1992;159-170
6. Claverie J.M., Bougueleret L. Heuristic informational analysis of sequences. Nucl. Acids Res. 14:1986;179-196
7. DeRisi J.L., Iyer V.R., Brown P.O. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science. 278:1997;680-686
8. Fondrat C., Kalogeropoulos A. Approaching the function of new genes by detection of their potential upstream activation sequences in Saccharomyces cerevisiae application to chromosome III. Curr. Genet. 25:1994;396-406
9. Galas D.J., Eggert M., Waterman M.S. Rigorous pattern-recognition methods for DNA sequences analysis of promoter sequences from Escherichia coli. J. Mol. Biol. 186:1985;117-128
10. Goffeau A. Molecular fish on chips. Nature. 385:1997;202-203
11. Guarente L. Messenger RNA transcription and its control in Saccharomyces cerevisiae. Jones E.W., Pringle J.R., Broach J.R. The Molecular and Cellular Biology of the Yeast Saccharomyces Gene Expression. 1992;193-281 Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
12. Gundavaram S. CGI Programming on the World Wide Web. 1996;O'Reilly Associates, Sebastopol, CA
13. Heinemeyer T., Wingender E., Reuter I., Hermjakob H., Kel A.E., Kel O.V., Ignatieva E.V., Ananko E.A., Podkolodnaya O.A., Kolpakov F.A., Podkolodny N.L., Kolchanov N.A. Databases on transcriptional regulation TRANSFAC, TRRD and COMPEL. Nucl. Acids Res. 26:1998;362-367
14. Hertz G.Z., Stormo G.D. Identification of consensus patterns in unaligned DNA and protein sequences a large-deviation statistical basis for penalizing gaps. Proceeds. 3rd Internat. Conf. on Bioinformatics and Genome Research. 1995;201-216 World Scientific Publishing Co. Ltd, Singapore
15. Hertz G.Z., Hartzell G.W., Stormo G.D. Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Comput. Appl. Biosci. 6:1990;81-92
16. Hinnebusch A.G. General and pathway-specific regulatory mechanisms controlling the synthesis of amino acid biosynthetic enzymes in Saccharomyces cerevisiae. Jones E.W., Pringle J.R., Broach J.R. The Molecular and Cellular Biology of the Yeast Saccharomyces Gene Expression. 1992;319-414 Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
17. Hutchinson G.B. The prediction of vertebrate promoter regions using differential hexamer frequency analysis. Comput. Appl. Biosci. 12:1996;391-398
18. Jauniaux J.C., Vandenbol M., Vissers S., Broman K., Grenson M. Nitrogen catabolite regulation of proline permease in Saccharomyces cerevisiae. Cloning of the PUT4 gene and study of PUT4 RNA levels in wild-type and mutant strains. Eur. J. Biochem. 164:1987;601-606
19. Johnston M., Carlson M. Regulation of carbon and phosphate utilisation. Jones E.W., Pringle J.R., Broach J.R. The Molecular and Cellular Biology of the Yeast Saccharomyces Gene Expression. 1992;193-281 Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
20. Jones E.W., Pringle J.R., Broach J.R. The Molecular and Cellular Biology of the Yeast Saccharomyces Gene Expression. 1992;Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
21. Kleffe J., Borodovsky M. First and second moment counts of words in random texts generated by Markov chains. Comput. Appl. Biosci. 8:1992;433-441
22. Lashkari D.A., DeRisi J.L., McCusker J.H., Namath A.F., Gentile C., Hwang S.Y., Brown P.O., Davis R.W. Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc. Natl Acad. Sci. USA. 94:1997;13057-13062
23. Lawrence C.E., Reilly A.A. An expectation maximisation (EM) algorithm for the identification and characterisation of common sites in unaligned biopolymer sequences. Proteins Struct. Funct. Genet. 7:1990;41-51
24. Lawrence C.E., Altschul S.F., Boguski M.S., Liu J.S., Neuwald A.F., Wootton J.C. Detecting subtle signals a Gibbs sampling strategy for multiple alignment. Science. 262:1993;208-214
25. Magasanik B. Regulation of nitrogen utilisation. Jones E.W., Pringle J.R., Broach J.R. The Molecular and Cellular Biology of the Yeast Saccharomyces Gene Expression. 1992;283-318 Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
26. Mengeritsky G., Smith T.F. Recognition of characteristic patterns in sets of functionally equivalent DNA sequences. Comput. Appl. Biosci. 3:1987;223-227
27. Naus J.I., Sheng K.-N. Matching among multiple random sequences. Bull. Mat. Biol. 59:1997;483-496
28. Neidhardt F.C., Savageau M.A. Regulation beyond the operon. Curtis R. Escherichia coli and Salmonella Cellular and Molecular Biology. 1996;1325-1342 ASM Press, Washington. et al
29. Neuwald A.F., Liu J.S., Lawrence C.E. Gibbs motif sampling detection of bacterial outer membrane protein repeats. Protein Sci. 4:1995;1618-1632
30. Oshima Y., Ogawa N., Harashima S. Regulation of phosphatase synthesis in Saccharomyces cerevisiae a review. Gene. 179:1996;171-177
31. Paltauf F., Kohlwein S.D., Henry S. Regulation and compartmentalization of lipid synthesis in yeast. Jones E.W., Pringle J.R., Broach J.R. The Molecular and Cellular Biology of the YeastSaccharomyces Gene Expression. 1992;415-500 Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
32. Pevzner P.A., Borodovsky M.Y., Mironov A.A. Linguistics of nucleotide sequences I the significance of deviations from the mean statistical characteristics and prediction of the frequencies of occurrence of words. J. Biomol. Struct.Dynam. 6:1989;1013-1026
33. Schena M. Genome analysis with gene expression microarrays. BioEssays. 18:1996;427-431
34. Schena M., Shalon D., Davis R.W., Brown P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 270:1995;467-470
35. Schena M., Shalon D., Heller R., Chai A., Brown P.O., Davis R.W. Parallel human genome analysis microarray-based expression monitoring of 1000 genes. Proc. Natl Acad. Sci. USA. 93:1996;10614-10619
36. Stormo G.D., Hartzell G.W. Identifying protein-binding sites from unaligned DNA fragments. Proc. Natl Acad. Sci. USA. 86:1989;1183-1187
37. Strachan T., Abitol M., Davidson D., Beckman J.S. A new dimension for the human genome project towards comprehensive expression maps. Nature Genet. 16:1997;126-132
38. Stückle E.E., Emmrich C., Grob U., Nielsen P.J. Statistical analysis of nucleotide sequences. Nucl. Acids Res. 18:1990;6641-6647
39. Velculescu V.E., Zhang L., Zhou W., Vogelstein J., Basrai M.A., Basset D.E. Jr, Hieter P., Vogelstein B., Kinzler K.W. Characterisation of the yeast transcriptome. Cell. 88:1997;243-251
40. Wall L., Schwartz R.L. Programming Perl. 1991;O'Reilly and Associates, Inc, Sebastopol, CA
41. Waterman M.S., Arratia R., Galas D.J. Pattern recognition in several sequences consensus and alignment. Bull. Math. Biol. 45:1984;515-527
42. Wingender E., Dietze P., Karas H., Knuppel R. TRANSFAC a database on transcription factors and their DNA binding sites. Nucl. Acids Res. 24:1996;238-241
43. Wingender E., Kel A.E., Kel O.V., Karas H., Heinemeyer T., Dietze P., Knüppel R., Romaschenko A.G., Kolchanov N.A. TRANSFAC, TRRD and COMPEL towards a federated database system on transcriptional regulation. Nucl. Acids Res. 25:1997;265-268
44. Wolfertstetter F., Frech K., Hermann G., Werner T. Identification of functional elements in unaligned nucleic acid sequences by a novel tuple search algorithm. Comput. Appl. Biosci. 12:1996;71-80
45. Yagil G. The frequency of oligopurine. oligopyrimidine and other two-base tracts in yeast chromosome III. Yeast. 10:1994;601-611