Quantitative inference of dynamic regulatory pathways via microarray data

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  Chang, Wen Chieh ^a   Li, Chang Wei ^a   Chen, Bor Sen ^a  

^a NATIONAL TSING HUA UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS THALIANA; CAUSAL RELATIONSHIPS; DYNAMIC MODELING APPROACH; DYNAMIC REGULATORY PATHWAYS; PHYSICAL INTERACTIONS; REGULATORY FUNCTIONS; SECOND-ORDER DYNAMIC MODEL; YEAST SACCHAROMYCES CEREVISIAE;

DYNAMICS; INFERENCE ENGINES; ITERATIVE METHODS; METABOLISM; PIGMENTS; SIGNALING; YEAST;

GENE EXPRESSION;

CYTOCHROME; PHYTOCHROME; DNA BINDING PROTEIN; PROTEIN BINDING; SACCHAROMYCES CEREVISIAE PROTEIN; TRANSCRIPTION FACTOR;

ARABIDOPSIS; ARTICLE; BIOLOGICAL RHYTHM; CELL COMMUNICATION; CELL RESPIRATION; CIRCADIAN RHYTHM; DNA FLANKING REGION; DNA MICROARRAY; FERMENTATION; FUNGAL METABOLISM; GENE CONTROL; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE IDENTIFICATION; GENE INTERACTION; GENE TARGETING; GENETIC ALGORITHM; MOLECULAR PHYLOGENY; NONHUMAN; PERFORMANCE; PHOTOPERIODICITY; PROCESS DESIGN; QUANTITATIVE ANALYSIS; REGULATOR GENE; REGULATORY MECHANISM; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION; VALIDATION PROCESS; ALGORITHM; BIOLOGICAL MODEL; BIOLOGY; CHEMISTRY; COMPUTER SIMULATION; DEVICES; FUNGAL GENE; FUNGAL GENOME; GENE EXPRESSION REGULATION; METABOLISM; PLANT GENE; PROCEDURES; PROTEIN ANALYSIS; STATISTICAL MODEL;

ARABIDOPSIS THALIANA; SACCHAROMYCES CEREVISIAE;

ALGORITHMS; ARABIDOPSIS; CIRCADIAN RHYTHM; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DNA-BINDING PROTEINS; FERMENTATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; GENES, PLANT; GENOME, FUNGAL; LIKELIHOOD FUNCTIONS; MODELS, BIOLOGICAL; MODELS, STATISTICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTORS;

EID: 25444464334     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-44     Document Type: Article

References (66)

1. Kettman JR, Frey JR, Lefkovits I: Proteome, transcriptome and genome: top down or bottom up analysis. Biomol Eng 2001, 18:207-212.
2. Scheel J, Von Brevern MC, Horlein A, Fischer A, Schneider A, Bach A: Yellow pages to the transcriptome. Pharmacogenomics 2002, 3:791-807.
3. Velculescu VE, Zhang L, Zhou W, Vogelstein J, Basrai MA, Bassett DE Jr, Hieter P, Vogelstein B, Kinzler KW: Characterization of the yeast transcriptome. Cell 1997, 88:243-251.
4. Eastmond PJ, Graham IA: Trehalose metabolism: a regulatory role for trehalose-6-phosphate. Curr Opin Plant Biol 2003, 6:231-235.
5. Harkin DP: Uncovering Functionally Relevant Signaling Pathways Using Microarray-Based Expression Profiles. The Oncologist 2000, 5:511-517.
6. Verdone L, Cesari F, Denis CL, Di Mauro E, Caserta M: Factors affecting Saccharomyces cerevisiae ADH2 chromatin remodeling and transcription. J Biol Chem 1997, 272:30828-30834.
7. Yanovsky MJ, Kay SA: Signaling networks in the plant circadian system. Curr Opin Plant Biol 2001, 4:429-435.
8. Sontag E, Kiyatkin A, Kholodenko BN: Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data. Bioinformatics 2004, 20:1877-86.
9. Schena M, Shalon D, Davis RW, Brown PO: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270:467-470.
10. Lipshutz RJ, Fodor SP, Gingeras TR, Lockhart DJ: High density synthetic olignucleotide arrays. Nat Gentet 1999, 21:20-24.
11. Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC, Dwight SS, Kaloper M, Weng S, Jin H, Ball CA, Eisen MB, Spellman PT, Brown PO, Botstein D, Cherry JM: The Stanford Microarray Database. Nucleic Acids Res 2001, 29:152-155.
12. Edgar R, Domrachev M, Lash AE: Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002, 30:207-210.
13. Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA: ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Res 2003, 31:68-71.
14. 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.
15. Harmer SL, Hogenesch JB, Straume M, Chang HS, Han B, Zhu T, Wang X, Kreps JA, Kay SA: Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 2000, 290:2110-2113.
16. Schaffer R, Landgraf J, Accerbi M, Simon V, Larson M, Wisman E: Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis. Plant Cell 2001, 13:113-123.
17. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PQ, Bostein D, Futcher B: Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cererisiae by microarray hybridization. Mol Biol Cell 1998, 9:3273-3297.
18. 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.
19. Gasch AP, Eisen MB: Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biol 2002, 3:RESEARCH0059.
20. Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR: Interpreting patterns of gene expression with self- organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA 1999, 96:2907-2912.
21. Alter O, Brown PO, Botstein D: Singular value decomposition for genome- wide expression data processing and modeling. Proc Natl Acad Sci USA 2000, 97:10101-10106.
22. Brown MP, Grundy WN, Lin D, Cristianini N, Sugnet CW, Furey TS, Ares M Jr, Haussler D: Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci U S A 2000, 97:262-267.
23. Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM: Systematic determination of genetic network architecture. Nat Genet 1999, 22:281-285.
24. Friedman N, Linial M, Nachman I, Pe'er D: Using Bayesian networks to analyze expression data. J Comput Biol 2000, 7:601-620.
25. Husmeier D: Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks. Bioinformatics 2003, 19:2271-82.
26. Huang S: Gene expression profiling, genetic networks, and cellular states: an integrating concept for tumorigenesis and drug discovery. J Mol Med 1999, 7:469-480.
27. Chen HC, Lee HC, Lin TY, Li WH, Chen BS: Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle. Bioinformatics 2004, 20:1914-1927.
28. Michael TP, McClung CR: Phase-specific circadian clock regulatory elements in Arabidopsis. Plant Physiol 2002, 130:627-638.
29. Motaki S, Ayako K, Kazuko YS, Kazuo S: Molecular response to drought, salinity and frost: common and different paths for plant protection. Curr Opin Biotechnol 2003, 14:194-199.
30. DeRisi JL, Iyer VR, Brown PO: Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 1997, 278:680-686.
31. Staiger D: Circadian rhythms in Arabidopsis: time for nuclear proteins. Planta 2002, 214:334-344.
32. Somers DE, Devlin PF, Kay SA: Phytochromes and cryptochromes in the entrainment of the Arabidopsis circadian clock. Science 1998, 282:1488-1490.
33. Flores CL, Rodriguez C, Petit T, Gancedo C: Carbohydrate and energy- yielding metabolism in non-conventional yeasts. FEMS Microbiol Rev 2000, 24:517-529.
34. Deng XW, Quail PH: Signalling in light-controlled development. Semin Cell Dev Biol 1999, 10:121-129.
35. Eriksson ME, Hanano S, Southern MM, Hall A, Millar AJ: Response regulator homologues have complementary, light-dependent functions in the Arabidopsis circadian clock. Planta 2003, 218:159-162.
36. Green RM, Tingay S, Wang ZY, Tobin EM: Circadian rhythms confer a higher level of fitness to Arabidopsis plants. Plant Physiol 2002, 129:576-584.
37. Hall A, Kozma-Bognar L, Bastow RM, Nagy F, Millar AJ: Distinct regulation of CAB and PHYB gene expression by similar circadian clocks. Plant J 2002, 32:529-537.
38. Hayama R, Coupland G: Shedding light on the circadian clock and the photoperiodic control of flowering. Curr Opin Plant Biol 2003, 6:13-19.
39. Carre IA: Day-length perception and the photoperiodic regulation of flowering in Arabidopsis. J Biol Rhythms 2001, 16:415-423.
40. Alabadi D, Oyama T, Yanovsky MJ, Harmon FG, Mas P, Kay SA: Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock. Science 2001, 293:880-883.
41. Yin Z, Hatton L, Brown AJ: Differential post-transcriptional regulation of yeast mRNAs in response to high and low glucose concentrations. Mol Microbiol 2000, 35:553-565.
42. Johansson R: System Modeling and Identification. Prentice-Hall, Englewood Cliffs; 1993.
43. Mas P, Alabadi D, Yanovsky MJ, Oyama T, Kay SA: Dual role of TOC1 in the control of circadian and photomorphogenic responses in Arabidopsis. Plant Cell 2003, 15:223-236.
44. Mazzella MA, Cerdan PD, Staneloni RJ, Casal JJ: Hierarchical coupling of phytochromes and cryptochromes reconciles stability and light modulation of Arabidopsis development. Development 2001, 128:2291-2299.
45. Ohlmeier S, Kastaniotis AJ, Hiltunen JK, Bergmann U: The yeast mitochondrial proteome, a study of fermentative and respiratory growth. J Biol Chem 2004, 279:3956-3979.
46. Somers DE: Clock-associated genes in Arabidopsis: a family affair. Philos Trans R Soc Lond B Biol Sci 2001, 356:1745-1753.
47. Valverde F, Mouradov A, Soppe W, Ravenscroft D, Samach A, Coupland G: Photoreceptor regulation of CONSTANS protein in photoperiodic flowering. Science 2004, 303:1003-1006.
48. Mas P, Devlin PF, Panda S, Kay SA: Functional interaction of phytochrome B and cryptochrome 2. Nature 2000, 408:207-211.
49. Sharrock RA, Clack T: Patterns of expression and normalized levels of the five Arabidopsis phytochromes. Plant Physiol 2002, 130:442-456.
50. Fankhauser C, Staiger D: Photoreceptors in Arabidopsis thaliana: light perception, signal transduction and entrainment of the endogenous clock. Planta 2002, 216:1-16.
51. Toth R, Kevei E, Hall A, Millar AJ, Nagy F, Kozma-Bognar L: Orcadian clock-regulated expression of phytochrome and cryptochrome genes in Arabidopsis. Plant Physiol 2001, 127:1607-1616.
52. Ahmad M, Jarillo JA, Smirnova O, Cashmore AR: The CRY1 blue light photoreceptor of Arabidopsis interacts with phytochrome A in vitro. Mol Cell 1998, 1:939-948.
53. Casal JJ: Phytochromes, cryptochromes, phototropin: photoreceptor interactions in plants. Photochem Photobiol 2000, 71:1-11.
54. Hall A, Kozma-Bognar L, Toth R, Nagy F, Millar AJ: Conditional circadian regulation of PHYTOCHROME A gene expression. Plant Physiol 2001, 127:1808-1818.
55. Martinez-Garcia JF, Huq E, Quail PH: Direct targeting of light signals to a promoter element-bound transcription factor. Science 2000, 288:859-863.
56. Carre IA, Kim JY: MYB transcription factors in the Arabidopsis circadian clock. J Exp Bot 2002, 53:1551-1557.
57. Kim JY, Song HR, Taylor BL, Carre IA: Light-regulated translation mediates gated induction of the Arabidopsis clock protein LHY. EMBO J 2003, 22:935-944.
58. Imaizumi T, Tran HG, Swartz TE, Briggs WR, Kay SA: FKF1 is essential for photoperiodic-specific light signalling in Arabidopsis. Nature 2003, 426:302-306.
59. Barnett JA: A history of research on yeasts 6: the main respiratory pathway. Yeast 2003, 20:1015-1044.
60. de Mesquita JF, Zaragoza O, Gancedo JM: Functional analysis of upstream activating elements in the promoter of the FBP1 gene from Saccharomyces cerevisiae. Curr Genet 1998, 33:406-411.
61. Dickinson FM, Back S: The activity of yeast ADH I and ADH II with long- chain alcohols and diols. Chem Biol Interact 2001, 130-132((1-3)):417-423.
62. Dickinson JR, Salgado LE, Hewlins MJ: The catabolism of amino acids to long chain and complex alcohols in Saccharomyces cerevisiae. Biol Chem 2003, 278:8028-8034.
63. Fraenkel DG: The top genes: on the distance from transcript to function in yeast glycolysis. Curr Opin Microbiol 2003, 6:198-201.
64. Goncalves PM, Griffioen G, Bebelman JP, Planta RJ: Signalling pathways leading to transcriptional regulation of genes involved in the activation of glycolysis in yeast. Mol Microbiol 1997, 25:483-493.
65. Goncalves P, Planta RJ: Starting up yeast glycolysis. Trends Microbiol 1998, 6:314-319.
66. Scheffler IE, de la Cruz BJ, Prieto S: Control of mRNA turnover as a mechanism of glucose repression in Saccharomyces cerevisiae. Int J Biochem Cell Biol 1998, 30:1175-1193.