Enriching for direct regulatory targets in perturbed gene-expression profiles

Genome Biology

Volumn 5, Issue 4, 2004, Pages

  Tringe, Susannah G ^a,c   Wagner, Andreas ^b   Ruby, Stephanie W ^a  

^a UNIVERSITY OF NEW MEXICO HEALTH SCIENCES CENTER   (United States)

^b UNIVERSITY OF NEW MEXICO   (United States)

^c DOE JOINT GENOME INSTITUTE   (United States)

Author keywords

Additional Data File; Boolean Network; Double Mutant; Regulatory Relationship; Strong Component

Indexed keywords

FUNGAL DNA;

ALGORITHM; ARTICLE; ARTIFICIAL INTELLIGENCE; BIOLOGY; COMPUTER GRAPHICS; COMPUTER SIMULATION; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; METHODOLOGY; MUTATION; REGULATORY SEQUENCE; SACCHAROMYCES CEREVISIAE;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; COMPUTER SIMULATION; DATABASES, GENETIC; DNA, FUNGAL; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REGULATORY SEQUENCES, NUCLEIC ACID; SACCHAROMYCES CEREVISIAE;

EID: 4944246911     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2004-5-4-r29     Document Type: Article

References (49)

1. D'Haeseleer P, Liang S, Somogyi R: Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics 2000, 16:707–726. DOI: 10.1093/bioinformatics/16.8.707
2. de Jong H: Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol 2002, 9:67–103. DOI: 10.1089/10665270252833208
3. Lyons TJ, Gasch AP, Gaither LA, Botstein D, Brown PO, Eide DJ: Genome-wide characterization of the Zap1p zinc-responsive regulon in yeast. Proc Natl Acad Sci USA 2000, 97:7957–7962. DOI: 10.1073/pnas.97.14.7957
4. Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, et al.: Genome-wide location and function of DNA binding proteins. Science 2000, 290:2306–2309. DOI: 10.1126/science.290.5500.2306
5. Wagner A: How to reconstruct a large genetic network from n gene perturbations in fewer than n(2) easy steps. Bioinformatics 2001, 17:1183–1197. DOI: 10.1093/bioinformatics/17.12.1183
6. Griffiths AJF, Gelbart WM, Miller JH, Lewontin RC: Modern Genetic Analysis New York: WH Freeman 1999.
7. Avery L, Wasserman S: Ordering gene function: the interpretation of epistasis in regulatory hierarchies. Trends Genet 1992, 8:312–316. DOI: 10.1016/0168-9525(92)90263-4
8. Jarvik J, Botstein D: A genetic method for determining the order of events in a biological pathway. Proc Natl Acad Sci USA 1973, 70:2046–2050. DOI: 10.1073/pnas.70.7.2046
9. Harary F: Graph Theory Reading, MA: Perseus Books 1969.
10. Aho AV, Garey MR, Ullman JD: The transitive reduction of a directed graph. SIAM J Comput 1972, 1:131–137. DOI: 10.1137/0201008
11. Maki Y, Tominaga D, Okamoto M, Watanabe S, Eguchi Y: Development of a system for the inference of large scale genetic networks. Pac Symp Biocomput 2001, 446–458.
12. Becskei A, Serrano L: Engineering stability in gene networks by autoregulation. Nature 2000, 405:590–593. DOI: 10.1038/35014651
13. Rosenfeld N, Elowitz MB, Alon U: Negative autoregulation speeds the response times of transcription networks. J Mol Biol 2002, 323:785–793. DOI: 10.1016/S0022-2836(02)00994-4
14. Thieffry D, Huerta AM, Perez-Rueda E, Collado-Vides J: From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. BioEssays 1998, 20:433–440. DOI: 10.1002/(SICI)1521-1878(199805)20:5<433::AID-BIES10>3.0.CO;2-2
15. Guelzim N, Bottani S, Bourgine P, Kepes F: Topological and causal structure of the yeast transcriptional regulatory network. Nat Genet 2002, 31:60–63. DOI: 10.1038/ng873
16. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, et al.: Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 2002, 298:799–804. DOI: 10.1126/science.1075090
17. Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai H, He YD, et al.: Functional discovery via a compendium of expression profiles. Cell 2000, 102:109–126. DOI: 10.1016/S0092-8674(00)00015-5
18. Arthington-Skaggs BA, Crowell DN, Yang H, Sturley SL, Bard M: Positive and negative regulation of a sterol biosynthetic gene (ERG3) in the post-squalene portion of the yeast ergosterol pathway. FEBS Lett 1996, 392:161–165. DOI: 10.1016/0014-5793(96)00807-1
19. Smith SJ, Crowley JH, Parks LW: Transcriptional regulation by ergosterol in the yeast Saccharomyces cerevisiae. Mol Cell Biol 1996, 16:5427–5432. DOI: 10.1128/MCB.16.10.5427
20. Vik A, Rine J: Upc2p and Ecm22p, dual regulators of sterol biosynthesis in Saccharomyces cerevisiae. Mol Cell Biol 2001, 21:6395–6405. DOI: 10.1128/MCB.21.19.6395-6405.2001
21. Deckert J, Torres AM, Hwang SM, Kastaniotis AJ, Zitomer RS: The anatomy of a hypoxic operator in Saccharomyces cerevisiae. Genetics 1998, 150:1429–1441.
22. Hongay C, Jia N, Bard M, Winston F: Mot3 is a transcriptional repressor of ergosterol biosynthetic genes and is required for normal vacuolar function in Saccharomyces cerevisiae. EMBO J 2002, 21:4114–4124. DOI: 10.1093/emboj/cdf415
23. Henry KW, Nickels JT, Edlind TD: ROX1 and ERG regulation in Saccharomyces cerevisiae: implications for antifungal susceptibility. Eukaryot Cell 2002, 1:1041–1044. DOI: 10.1128/EC.1.6.1041-1044.2002
24. Guetsova ML, Lecoq K, Daignan-Fornier B: The isolation and characterization of Saccharomyces cerevisiae mutants that constitutively express purine biosynthetic genes. Genetics 1997, 147:383–397.
25. Rebora K, Desmoucelles C, Borne F, Pinson B, Daignan-Fornier B: Yeast AMP pathway genes respond to adenine through regulated synthesis of a metabolic intermediate. Mol Cell Biol 2001, 21:7901–7912. DOI: 10.1128/MCB.21.23.7901-7912.2001
26. Rodriguez-Navarro S, Igual JC, Perez-Ortin JE: SRC1: an intron-containing yeast gene involved in sister chromatid segregation. Yeast 2002, 19:43–54. DOI: 10.1002/yea.803
27. Shen-Orr SS, Milo R, Mangan S, Alon U: Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 2002, 31:64–68. DOI: 10.1038/ng881
28. Simon I, Barnett J, Hannett N, Harbison CT, Rinaldi NJ, Volkert TL, Wyrick JJ, Zeitlinger J, Gifford DK, Jaakkola TS, et al.: Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 2001, 106:697–708. DOI: 10.1016/S0092-8674(01)00494-9
29. Aalfs JD, Kingston RE: What does 'chromatin remodeling' mean? Trends Biochem Sci 2000, 25:548–555. DOI: 10.1016/S0968-0004(00)01689-3
30. Olson KA, Nelson C, Tai G, Hung W, Yong C, Astell C, Sadowski I: Two regulators of Ste12p inhibit pheromone-responsive transcription by separate mechanisms. Mol Cell Biol 2000, 20:4199–4209. DOI: 10.1128/MCB.20.12.4199-4209.2000
31. Kent NA, Karabetsou N, Politis PK, Mellor J: In vivo chromatin remodeling by yeast ISWI homologs Isw1p and Isw2p. Genes Dev 2001, 15:619–626. DOI: 10.1101/gad.190301
32. Akutsu T, Kuhara S, Maruyama O, Miyano S: A system for identifying genetic networks from gene expression patterns produced by gene disruptions and overexpressions. Genome Inform Ser Workshop Genome Inform 1998, 9:151–160.
33. Kyoda KM, Morohashi M, Onami S, Kitano H: A gene network inference method from continuous-value gene expression data of wild-type and mutants. Genome Inform Ser Workshop Genome Inform 2000, 11:196–204.
34. Ideker TE, Thorsson V, Karp RM: Discovery of regulatory interactions through perturbation: inference and experimental design. Pac Symp Biocomput 2000, 5:305–316.
35. Pe'er D, Regev A, Elidan G, Friedman N: Inferring subnetworks from perturbed expression profiles. Bioinformatics 2001, 17:S215-S224. DOI: 10.1093/bioinformatics/17.suppl_1.S215
36. Yoo C, Thorsson V, Cooper GF: Discovery of causal relationships in a gene-regulation pathway from a mixture of experimental and observational DNA microarray data. Pac Symp Biocomput 2002, 498–509.
37. Friedman N, Linial M, Nachman I, Pe'er D: Using Bayesian networks to analyze expression data. J Comput Biol 2000, 7:601–620. DOI: 10.1089/106652700750050961
38. Zupan B, Demsar J, Bratko I, Juvan P, Halter JA, Kuspa A, Shaulsky G: GenePath: a system for automated construction of genetic networks from mutant data. Bioinformatics 2003, 19:383–389. DOI: 10.1093/bioinformatics/btf871
39. Neigeborn L, Carlson M: Mutations causing constitutive invertase synthesis in yeast: genetic interactions with snf mutations. Genetics 1987, 115:247–253.
40. Trumbly RJ: Glucose repression in the yeast Saccharomyces cerevisiae. Mol Microbiol 1992, 6:15–21. DOI: 10.1111/j.1365-2958.1992.tb00832.x
41. Kamath RS, Fraser AG, Dong Y, Poulin G, Durbin R, Gotta M, Kanapin A, Le Bot N, Moreno S, Sohrmann M, et al.: Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 2003, 421:231–237. DOI: 10.1038/nature01278
42. Chory J, Ecker JR, Briggs S, Caboche M, Coruzzi GM, Cook D, Dangl J, Grant S, Guerinot ML, Henikoff S, et al.: National Science Foundation-Sponsored Workshop Report: "The 2010 Project" functional genomics and the virtual plant. A blueprint for understanding how plants are built and how to improve them. Plant Physiol 2000, 123:423–426. DOI: 10.1104/pp.123.2.423
43. Spradling AC, Stern D, Beaton A, Rhem EJ, Laverty T, Mozden N, Misra S, Rubin GM: The Berkeley Drosophila Genome Project gene disruption project: single P-element insertions mutating 25% of vital Drosophila genes. Genetics 1999, 153:135–177.
44. Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A, Anderson K, Andre B, et al.: Functional profiling of the Saccharomyces cerevisiae genome. Nature 2002, 418:387–391. DOI: 10.1038/nature00935
45. Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, Andre B, Bangham R, Benito R, Boeke JD, Bussey H, et al.: Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 1999, 285:901–906. DOI: 10.1126/science.285.5429.901
46. Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Page N, Robinson M, Raghibizadeh S, Hogue CW, Bussey H, et al.: Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 2001, 294:2364–2368. DOI: 10.1126/science.1065810
47. Mangan S, Alon U: Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci USA 2003, 100:11980–11985. DOI: 10.1073/pnas.2133841100
48. Newman ME, Strogatz SH, Watts DJ: Random graphs with arbitrary degree distributions and their applications. Phys Rev E Stat Nonlin Soft Matter Phys 2001, 64:026118. DOI: 10.1103/PhysRevE.64.026118
49. West DB: Introduction to Graph Theory Upper Saddle River, NJ: Prentice Hall 2001.