Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes

Functional and Integrative Genomics

Volumn 3, Issue 3, 2003, Pages 125-134

  Sandelin, Albin ^a   Höglund, Annette ^a,b   Lenhard, Boris ^a   Wasserman, Wyeth W ^a,c  

^a KAROLINSKA INSTITUTE   (Sweden)

^b SAARLAND UNIVERSITY   (Germany)

^c UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

Genomics; Microarray; Pattern comparison; Pattern discovery; Transcription

Indexed keywords

DNA BINDING PROTEIN; FUNGAL DNA; REGULATOR PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR MCB; UNCLASSIFIED DRUG;

ALGORITHM; ARTICLE; BINDING SITE; CELL CYCLE; DNA DAMAGE; FUNGAL GENETICS; GENE CLUSTER; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; REGULATORY SEQUENCE; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS; DNA SEQUENCE; GENETICS; METABOLISM; METHODOLOGY; MULTIGENE FAMILY; PHYSIOLOGY;

ALGORITHMS; BINDING SITES; CELL CYCLE; DNA DAMAGE; MULTIGENE FAMILY; PROMOTER REGIONS (GENETICS); SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION FACTORS;

EID: 0346230985     PISSN: 1438793X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10142-003-0086-6     Document Type: Article

References (54)

1. Altschul SF, et al (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402 9254694
2. Blanchette M, Sinha S (2001) Separating real motifs from their artifacts. Bioinformatics 17 Suppl 1:S30-S38
3. Brazma A, et al (1998) Approaches to the automatic discovery of patterns in biosequences. J Comput Biol 5:279-305 1:CAS:528:DyaK1cXksFyhsbw%3D
4. Bussemaker HJ, et al (2001) Regulatory element detection using correlation with expression. Nat Genet 27:167-171 1:CAS:528:DC%2BD3MXhtFGktLk%3D
5. Chiang DY, et al (2001) Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles. Bioinformatics 17 Suppl 1:S49-S55
6. Cho RJ, et al (1998) A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell 2:65-73 1:CAS:528:DyaK1cXltVektLw%3D
7. Cliften PF, et al (2001) Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res 11:1175-1186 10.1101/gr.182901
8. Devaux F, et al (2002) Genome-wide studies on the nuclear PDR3-controlled response to mitochondrial dysfunction in yeast. FEBS Lett 515:25-28 10.1016/S0014-5793(02)02387-6
9. Elledge SJ (1996) Cell cycle checkpoints: Preventing an identity crisis. Science 274:1664-1672 1:CAS:528:DyaK28XntlyktL0%3D
10. Fickett JW (1996) Quantitative discrimination of MEF2 sites. Mol Cell Biol 16:437-441
11. Gasch AP, et al (2001) Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p. Mol Biol Cell 12:2987-3003 1:CAS:528:DC%2BD3MXns1Chsbg%3D
12. Gavin AC, et al (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141-147 1:CAS:528:DC%2BD38XmsVCgtw%3D%3D
13. Getz G, et al (2000) Super-paramagnetic clustering of yeast gene expression profiles. Physica A 279:457-464 10.1016/S0378-4371(99)00524-5
14. Giaever G, et al (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418:387-391
15. Goffeau A, et al (1996) Life with 6000 genes. Science 274:546,563-546,547 1:CAS:528:DyaK28XmsVWlt7k%3D
16. Halfon MS, Michelson AM (2002) Exploring genetic regulatory networks in metazoan development: Methods and models. Physiol Genomics 10:131-143 1:CAS:528:DC%2BD38XnvV2gu7c%3D
17. Helden J van, et al (1998) Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J Mol Biol 281:827-842 10.1006/jmbi.1998.1947
18. Helden J van, et al (2000) A web site for the computational analysis of yeast regulatory sequences. Yeast 16:177-187 10.1002/ (SICI)1097-0061(20000130)16:2<177::AID-YEA516>3.0.CO;2-9
19. Ho Y, et al (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415:180-183 1:CAS:528:DC%2BD38Xms1SnsA%3D%3D
20. Huang M, et al (1998) The DNA replication and damage checkpoint pathways induce transcription by inhibition of the Crt1 repressor. Cell 94:595-605 1:CAS:528:DyaK1cXmtVWksr4%3D
21. Hughes JD, et al (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 296:1205-1214 10.1006/ jmbi.2000.3519
22. Ideker T, et al (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 18 Suppl 1:S233-S240
23. Ito T, et al (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 98:4569-4574 1:CAS:528:DC%2BD3MXjtVagtLc%3D
24. Iyer VR, et al (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409:533-538 10.1038/35054095
25. Johnston LH, Johnson AL (1995) The DNA repair genes RAD54 and UNG1 are cell cycle regulated in budding yeast but MCB promoter elements have no essential role in the DNA damage response. Nucleic Acids Res 23:2147-2152 7610042
26. Kim J, et al (1993) Adaptability at the protein-DNA interface is an important aspect of sequence recognition by bZIP proteins. Proc Natl Acad Sci USA 90:4513-4517 1:CAS:528:DyaK3sXks1Crsr0%3D
27. Lawrence CE, Reilly AA (1990) An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins 7:41-51 1:CAS:528:DyaK3cXitFWquro%3D
28. Lawrence CE, et al (1993) Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment. Science 262:208-214 1:CAS:528:DyaK3sXms1Gjsrk%3D
29. Lee TI, et al (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298:799-804 10.1126/science.1075090
30. Lenhard B, Wasserman WW (2002) TFBS: Computational framework for transcription factor binding site analysis. Bioinformatics 18:1135-1136 10.1093/bioinformatics/18.8.1135
31. Mewes HW, et al (2002) MIPS: A database for genomes and protein sequences. Nucleic Acids Res 30:31-34 1:CAS:528:DC%2BD38Xht12ksbg%3D
32. Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48:443-453 1:CAS:528:DyaE3cXktVShu74%3D
33. Pe'er D, et al (2001) Inferring subnetworks from perturbed expression profiles. Bioinformatics 17 Suppl 1:S215-S224
34. Pietrokovski S (1996) Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Acids Res 24:3836-3845 10.1093/nar/24.19.3836
35. Remacle JE, et al (1999) New mode of DNA binding of multi-zinc finger transcription factors: DeltaEF1 family members bind with two hands to two target sites. EMBO J 18:5073-5084 10.1093/emboj/18.18.5073
36. Ren B, et al (2000) Genome-wide location and function of DNA binding proteins. Science 290:2306-2309 10.1126/science.290.5500.2306
37. Ribeiro RC, et al (1995) The nuclear hormone receptor gene superfamily. Annu Rev Med 46:443-453 10.1146/annurev.med.46.1.443
38. Roth FP, et al (1998) Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol 16:939-945
39. Schneider TD, et al (1986) Information content of binding sites on nucleotide sequences. J Mol Biol 188:415-431 1:CAS:528:DyaL28XktF2rsbk%3D
40. Segal E, et al (2001) Rich probabilistic models for gene expression. Bioinformatics 17 Suppl 1:S243-S252
41. Segal E, et al (2003) Genome-wide discovery of transcriptional modules from DNA sequence and gene expression. Bioinformatics (in press)
42. Shannon MF, Rao S (2002) Transcription. Of chips and ChIPs. Science 296:666-669 10.1126/science.1062936
43. Shoemaker DD, et al (1996) Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. Nat Genet 14:450-456 1:CAS:528:DyaK28XntlGgt7k%3D
44. Sinha S, Tompa M (2002) Discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Res 30:5549-5560 10.1093/nar/gkf669
45. Spellman PT, et al (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9:3273-3297 1:CAS:528:DyaK1cXnvFOmt7Y%3D
46. Stajich JG, et al (2002) The Bioperl toolkit: Perl modules for life sciences. Genome Res 12:1611-1618 10.1101/gr.361602
47. Stapley BJ, et al (2002) Predicting the sub-cellular location of proteins from text using support vector machines. Pac Symp Biocomput 374-385
48. Stormo GD (2000) DNA binding sites: Representation and discovery. Bioinformatics 16:16-23
49. Thijs G, et al (2002) A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. J Comput Biol 9:447-464 10.1089/10665270252935566
50. Uetz P, et al (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403:623-627 1:CAS:528:DC%2BD3cXht1Oqsr0%3D
51. White S, et al (2001) The role of DSC1 components cdc10+, rep1+ and rep2+ in MCB gene transcription at the mitotic G1-S boundary in fission yeast. Curr Genet 40:251-259 10.1007/s002940100248
52. Winzeler EA, et al (1999) Fluorescence-based expression monitoring using microarrays. Methods Enzymol 306:3-18 1:CAS:528:DyaK1MXmsFOks7o%3D
53. Yuan D, et al (1999) Recognition of multiple patterns of DNA sites by Drosophila homeodomain protein Bicoid. J Biochem (Tokyo) 125:809-817
54. Zhu J, Zhang MQ (1999) SCPD: A promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics 15:607-611 10.1093/ bioinformatics/15.7.607