Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts

Genome Biology

Volumn 4, Issue 7, 2003, Pages

  Chiang, Derek Y ^a   Moses, Alan M ^a   Kellis, Manolis ^b   Lander, Eric S ^b   Eisen, Michael B ^a,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

Additional Data File; Close Spacing; Gene Subset; Transcription Factor Binding Site; Word Pair

Indexed keywords

TRANSCRIPTION FACTOR;

ARTICLE; BINDING SITE; DNA SEQUENCE; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; METHODOLOGY; NUCLEOTIDE SEQUENCE; PHYLOGENY; REGULATORY SEQUENCE; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

BASE SEQUENCE; BINDING SITES; CONSERVED SEQUENCE; GENE EXPRESSION REGULATION, FUNGAL; PHYLOGENY; REGULATORY SEQUENCES, NUCLEIC ACID; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 0037811432     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2003-4-7-r43     Document Type: Article

References (52)

1. Composite regulatory elements: structure, function and classification. [http://www.gene-regulation.com/pub/databases/transcompel/compel.html]
2. Wolberger C: Multiprotein-DNA complexes in transcriptional regulation. Annu Rev Biophys Biomol Struct. 1999, 28: 29-56. 10.1146/annurev.biophys.28.1.29. DOI: 10.1146/annurev.biophys.28.1.29
3. Mead J, Bruning AR, Gill MK, Steiner AM, Acton TB, Vershon AK: Interactions of the Mcm1 MADS box protein with cofactors that regulate mating in yeast. Mol Cell Biol. 2002, 22: 4607-4621. 10.1128/MCB.22.13.4607-4621.2002. DOI: 10.1128/MCB.22.13.4607-4621.2002
4. Bhoite LT, Allen JM, Garcia E, Thomas LR, Gregory ID, Voth WP, Whelihan K, Rolfes RJ, Stillman DJ: Mutations in the Pho2 (Bas2) transcription factor that differentially affect activation with its partner proteins Bas1, Pho4, and Swi5. J Biol Chem. 2002, 277: 37612-37618. 10.1074/jbc.M206125200. DOI: 10.1074/jbc.M206125200
5. Blaiseau PL, Thomas D: Multiple transcriptional activation complexes tether the yeast activator Met4 to DNA. EMBO J. 1998, 17: 6327-6336. 10.1093/emboj/17.21.6327. DOI: 10.1093/emboj/17.21.6327
6. Gasch AP: The environmental stress response: a common yeast response to diverse environmental stresses. In Yeast Stress Responses. Edited by: Hohmann S, Mager WH. 2003, Berlin: Springer, 1: 11-70. DOI: 10.1007/3-540-45611-2_2
7. Vashee S, Melcher K, Ding WV, Johnston SA, Kodadek T: Evidence for two modes of cooperative DNA binding in vivo that do not involve direct protein-protein interactions. Curr Biol. 1998, 8: 452-458. DOI: 10.1016/S0960-9822(98)70179-4
8. Miller JA, Widom J: Collaborative competition mechanism for gene activation in vivo. Mol Cell Biol. 2003, 23: 1623-1632. 10.1128/MCB.23.5.1623-1632.2003. DOI: 10.1128/MCB.23.5.1623-1632.2003
9. Smith DL, Johnson AD: A molecular mechanism for combinatorial control in yeast: MCM1 protein sets the spacing and orientation of the homeodomains of an alpha 2 dimer. Cell. 1992, 68: 133-142. DOI: 10.1016/0092-8674(92)90212-U
10. Drazinic CM, Smerage JB, Lopez MC, Baker HV: Activation mechanism of the multifunctional transcription factor repressor-activator protein 1 (Rap1p). Mol Cell Biol. 1996, 16: 3187-3196. DOI: 10.1128/MCB.16.6.3187
11. Stormo GD: DNA binding sites: representation and discovery. Bioinformatics. 2000, 16: 16-23. 10.1093/bioinformatics/16.1.16. DOI: 10.1093/bioinformatics/16.1.16
12. Duret L, Bucher P: Searching for regulatory elements in human noncoding sequences. Curr Opin Struct Biol. 1997, 7: 399-406. 10.1016/S0959-440X(97)80058-9. DOI: 10.1016/S0959-440X(97)80058-9
13. Pennacchio LA, Rubin EM: Genomic strategies to identify mammalian regulatory sequences. Nat Rev Genet. 2001, 2: 100-109. 10.1038/35052548. DOI: 10.1038/35052548
14. Blanchette M, Tompa M: Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res. 2002, 12: 739-748. 10.1101/gr.6902. DOI: 10.1101/gr.6902
15. Loots GG, Ovcharenko I, Pachter L, Dubchak I, Rubin EM: rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res. 2002, 12: 832-839. 10.1101/gr.225502. Article published online before print in April 2002. DOI: 10.1101/gr.225502. Article published online before print in April 2002
16. Schwartz S, Zhang Z, Frazer KA, Smit A, Riemer C, Bouck J, Gibbs R, Hardison R, Miller W: PipMaker - a web server for aligning two genomic DNA sequences. Genome Res. 2000, 10: 577-586. 10.1101/gr.10.4.577. DOI: 10.1101/gr.10.4.577
17. Pilpel Y, Sudarsanam P, Church GM: Identifying regulatory networks by combinatorial analysis of promoter elements. Nat Genet. 2001, 29: 153-159. 10.1038/ng724. DOI: 10.1038/ng724
18. Bussemaker HJ, Li H, Siggia ED: Regulatory element detection using correlation with expression. Nat Genet. 2001, 27: 167-171. 10.1038/84792. DOI: 10.1038/84792
19. Keles S, van der Laan M, Eisen MB: Identification of regulatory elements using a feature selection method. Bioinformatics. 2002, 18: 1167-1175. 10.1093/bioinformatics/18.9.1167. DOI: 10.1093/bioinformatics/18.9.1167
20. Wang W, Cherry JM, Botstein D, Li H: A systematic approach to reconstructing transcription networks in Saccharomyces cerevisiae. Proc Natl Acad Sci USA. 2002, 99: 16893-16898. 10.1073/pnas.252638199. DOI: 10.1073/pnas.252638199
21. Conlon EM, Liu XS, Lieb JD, Liu JS: Integrating regulatory motif discovery and genome-wide expression analysis. Proc Natl Acad Sci USA. 2003, 100: 3339-3344. 10.1073/pnas.0630591100. DOI: 10.1073/pnas.0630591100
22. Wagner A: Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes. Bioinformatics. 1999, 15: 776-784. 10.1093/bioinformatics/15.10.776. DOI: 10.1093/bioinformatics/15.10.776
23. Klingenhoff A, Frech K, Quandt K, Werner T: Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity. Bioinformatics. 1999, 15: 180-186. 10.1093/bioinformatics/15.3.180. DOI: 10.1093/bioinformatics/15.3.180
24. Pavlidis P, Furey TS, Liberto M, Haussler D, Grundy WN: Promoter region-based classification of genes. Pac Symp Biocomput. 2001, 6: 151-164.
25. Kel-Margoulis OV, Ivanova TG, Wingender E, Kel AE: Automatic annotation of genomic regulatory sequences by searching for composite clusters. Pac Symp Biocomput. 2002, 7: 187-198.
26. Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES: Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature. 2003, 423: 241-254. 10.1038/nature01644. DOI: 10.1038/nature01644
27. Chiang DY, Brown PO, Eisen MB: Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles. Bioinformatics. 2001, 17: S49-S55. DOI: 10.1093/bioinformatics/17.suppl_1.S49
28. Cliften PF, Hillier LW, Fulton L, Graves T, Miner T, Gish WR, Waterston RH, Johnston M: Surveying Saccharomyces xs genomes to identify functional elements by comparative DNA sequence analysis. Genome Res. 2001, 11: 1175-1186. 10.1101/gr.182901. DOI: 10.1101/gr.182901
29. Zhu J, Zhang MQ: SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics. 1999, 15: 607-611. 10.1093/bioinformatics/15.7.607. DOI: 10.1093/bioinformatics/15.7.607
30. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO: Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell. 2000, 11: 4241-4257. DOI: 10.1091/mbc.11.12.4241
31. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B: Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell. 1998, 9: 3273-3297. DOI: 10.1091/mbc.9.12.3273
32. Cho RJ, Campbell MJ, Winzeler EA, Steinmetz L, Conway A, Wodicka L, Wolfsberg TG, Gabrielian AE, Landsman D, Lockhart DJ, et al: A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell. 1998, 2: 65-73. DOI: 10.1016/S1097-2765(00)80114-8
33. Gasch AP, Huang M, Metzner S, Botstein D, Elledge SJ, Brown PO: Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p. Mol Biol Cell. 2001, 12: 2987-3003. DOI: 10.1091/mbc.12.10.2987
34. Lee SE, Pellecioli A, Demeter J, Vaze MP, Gasch AP, Malkova A, Brown PO, Botstein D, Stearns T, Foiani M, et al: In Biological Responses to DNA Damage. 2000, Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 65: 303-314.
35. Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai HY, He YDD, et al: Functional discovery via a compendium of expression profiles. Cell. 2000, 102: 109-126. DOI: 10.1016/S0092-8674(00)00015-5
36. ® library, an integrated resource for protein information. Nucleic Acids Res. 2001, 29: 75-79. 10.1093/nar/29.1.75. DOI: 10.1093/nar/29.1.75
37. Causton HC, Ren B, Koh SS, Harbison CT, Kanin E, Jennings EG, Lee TI, True HL, Lander ES, Young RA: Remodeling of yeast genome expression in response to environmental changes. Mol Biol Cell. 2001, 12: 323-337. DOI: 10.1091/mbc.12.2.323
38. Hughes JD, Estep PW, Tavazoie S, Church GM: Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol. 2000, 296: 1205-1214. 10.1006/jmbi.2000.3519. DOI: 10.1006/jmbi.2000.3519
39. Thomas D, Surdin-Kerjan Y: Metabolism of sulfur amino acids in Saccharomyces cerevisiae. Microbiol Mol Biol Rev. 1997, 61: 503-532.
40. Fauchon M, Lagniel G, Aude JC, Lombardia L, Soularue P, Petat C, Marguerie G, Esentenac A, Werner M, Labarre J: Sulfur sparing in the yeast proteome in response to sulfur demand. Mol Cell. 2002, 9: 713-723. DOI: 10.1016/S1097-2765(02)00500-2
41. Williams RM, Primig M, Washburn BK, Winzeler EA, Bellis M, Sarrauste de Menthiere C, Davis RW, Esposito RE: The Ume6 regulon coordinates metabolic and meiotic gene expression in yeast. Proc Natl Acad Sci USA. 2002, 99: 13431-13436. 10.1073/pnas.202495299. DOI: 10.1073/pnas.202495299
42. Whitehead Institute Center for Genome Research - Yeast Comparative Genomics. [http://www-genome.wi.mit.edu/seq/Saccharomyces]
43. Vik A, Rine J: Upc2p and Ecm22p, dual regulators of sterol biosynthesis in Saccharomyces cerevisiae. Mol Cell Biol. 2001, 21: 6395-6405. 10.1128/MCB.21.19.6395-6405.2001. DOI: 10.1128/MCB.21.19.6395-6405.2001
44. Kwast KE, Burke PV, Poyton RO: Oxygen sensing and the transcriptional regulation of oxygen-responsive genes in yeast. J Exp Biol. 1998, 201: 1177-1195.
45. Liao GC, Rehm EJ, Rubin GM: Insertion site preferences of the P transposable element in Drosophila melanogaster. Proc Natl Acad Sci USA. 2000, 97: 3347-3351. 10.1073/pnas.050017397. DOI: 10.1073/pnas.97.7.3347
46. Berman BP, Nibu Y, Pfeiffer BD, Tomancek P, Celniker SE, Levine M, Rubin GM, Eisen MB: Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci USA. 2002, 99: 757-762. 10.1073/pnas.231608898. DOI: 10.1073/pnas.231608898
47. Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC, Dwight SS, Kaloper M, Weng S, Jin H, Ball CA, et al: The Stanford Microarray Database. Nucleic Acids Res. 2001, 29: 152-155. 10.1093/nar/29.1.152. DOI: 10.1093/nar/29.1.152
48. Benjamini Y, Hochberg Y: Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Statist Soc B. 1995, 57: 289-300.
49. Press WH, Teukolsky SA, Vertterling WT, Flannery BP: Numerical Recipes in C. 1992, Cambridge: Cambridge University Press, 2nd
50. Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA. 1998, 95: 14863-14868. 10.1073/pnas.95.25.14863. DOI: 10.1073/pnas.95.25.14863
51. The R Project for Statistical Computing. [http://www.r-project.org]
52. Eisen Lab. [http://rana.lbl.gov]