Dynamic modeling of cis-regulatory circuits and gene expression prediction via cross-gene identification

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  Lin, Li Hsieh ^a   Lee, Hsiao Ching ^a   Li, Wen Hsiung ^b,c   Chen, Bor Sen ^a  

^a NATIONAL TSING HUA UNIVERSITY   (Taiwan)

^b UNIVERSITY OF CHICAGO   (United States)

^c GENOMICS RESEARCH CENTER   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

EXPRESSION PROFILE; FUNCTIONAL ARCHITECTURE; GENE TRANSCRIPTIONS; IDENTIFICATION SCHEME; PROMOTER REGION; REGULATORY FUNCTIONS; TRADITIONAL APPROACHES; YEAST CELL CYCLES;

DYNAMIC MODELS; ELECTRIC NETWORK ANALYSIS; GENES;

TRANSCRIPTION;

CIS ACTING ELEMENT; TRANSCRIPTION FACTOR; CLB2 PROTEIN, S CEREVISIAE; CYCLIN B; LIPOPROTEIN; MFA2 PROTEIN, S CEREVISIAE; PHEROMONE; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; BIOINFORMATICS; CELL CYCLE; DNA MICROARRAY; GENE CONTROL; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENE NUMBER; GENETIC ALGORITHM; GENETIC TRANSCRIPTION; MATHEMATICAL COMPUTING; MOLECULAR MODEL; NONHUMAN; PREDICTION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; QUANTITATIVE ANALYSIS; YEAST CELL; BIOLOGICAL MODEL; CYTOLOGY; GENE EXPRESSION PROFILING; GENETICS; MULTIGENE FAMILY; PHYSIOLOGY; PROCEDURES; REGULATORY SEQUENCE; YEAST;

CELL CYCLE; CYCLIN B; GENE EXPRESSION PROFILING; LIPOPROTEINS; MODELS, GENETIC; MULTIGENE FAMILY; PHEROMONES; REGULATORY ELEMENTS, TRANSCRIPTIONAL; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION FACTORS; YEASTS;

EID: 27744485351     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-258     Document Type: Article

References (40)

1. Shea M, Ackers G: The OR control system of bacteriophage lambda. A physical-chemical model for gene- regulation. J Molec Biol 1985, 181:211-230.
2. Mjolsness E, Sharp DH, Reinitz J: A connectionist model of development. J Theoret Biol 1991, 152:429-453.
3. Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, Brown PO: Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 2001, 409:533-538.
4. Simon I, Barnett J, Hannett N, Harbison CT, Rinaldi NJ, Volkert TL, Wyrick JJ, Zeitlinger J, Gifford DK, Jaakkola TS, Young RA: Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 2001, 106:697-708.
5. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA: Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 2002, 298:799-804.
6. Gao F, Foat BC, Bussemaker HJ: Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. BMC Bioinformatics 2004, 5:31.
7. Wei H, Kaznessis Y. Inferring gene regulatory relationships by combining target-target pattern recognition and regulator-specific motif examination. Biotechnol Bioeng 2005; 89:53-77.
8. Haverty PM, Hansen U, Weng Z: Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification. Nucleic Acids Res 2004, 32:179-188.
9. Kato M, Hata N, Banerjee N, Futcher B, Zhang MQ: Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol 2004, 5:R56.
10. Nachman I, Regev A, Friedman N: Inferring quantitative models of regulatory networks from expression data. Bioinformatics 2004, 20:I248-I256.
11. Wang W, Cherry JM, Nochomovitz Y, Jolly E, Botstein D, Li H: Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation. Proc Natl Acad Sci USA 2005, 102:1998-2003.
12. Gardner TS, Cantor CR, Collins JJ: Construction of a genetic toggle switch in Escherichia coli. Nature 2000, 403:339-342.
13. Hasty J, Pradines J, Dolnik M, Collins JJ: Noise-based switches and amplifiers for gene expression. Proc Natl Acad Sci USA 2000, 97:2075-2080.
14. Hasty J, McMillen D, Collins JJ: Engineered gene circuits. Nature 2002, 420:224-230.
15. Tegner J, Yeung MK, Hasty J, Collins JJ: Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling. Proc Natl Acad Sci USA 2003, 100:5944-5949.
16. Yuh CH, Moore JG, Davidson EH: Quantitative functional interrelations within the cis-regulatory system of the S. purpuratus Endo16 gene. Development 1996, 122:4045-4056.
17. Yuh CH, Bolouri H, Davidson EH: Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene. Science 1998, 279:1896-1902.
18. Yuh CH, Bolouri H, Davidson EH: Cis-regulatory logic in the endo16 gene: switching from a specification to a differentiation mode of control. Development 2001, 128:617-629.
19. Banerjee N, Zhang MQ: Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Res 2003, 31:7024-7031.
20. Das D, Banerjee N, Zhang MQ: Interacting models of cooperative gene regulation. Proc Natl Acad Sci USA 2004, 101:16234-16239.
21. 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.
22. 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.
23. Michaelis S, Herskowitz I: The a-factor pheromone of Saccharomyces cerevisiae is essential for mating. Mol Cell Biol 1988, 8:1309-1318.
24. Wang Y, Liu CL, Storey JD, Tibshirani RJ, Herschlag D, Brown PO: Precision and functional specificity in mRNA decay. Proc Natl Acad Sci USA 2002, 99:5860-6865.
25. de Boor C: A Practical Guide to Splines. New York: Springer-Verlag Press; 1978.
26. Bar-Joseph Z, Gerber G, Gifford DK, Jaakkola TS, Simon I: A new approach to analyzing gene expression time series data. In The Sixth Annual International Conference on Research in Computational Molecular Biology (RECOMB): 39-48 2002; Washington DC.
27. Maher M, Cong F, Kindelberger D, Nasmyth K, Dalton S: Cell cycle-regulated transcription of the CLB2 gene is dependent on Mcm1 and a ternary complex factor. Mol Cell Biol 1995, 15:3129-3137.
28. Koranda M, Schleiffer A, Endler L, Ammerer G: Fork-head-like transcription factors recruit Ndd1 to the chromatin of G2/M-specific promoters. Nature 2000, 406:94-98.
29. Zhu G, Spellman PT, Volpe T, Brown PO, Botstein D, Davis TN, Futcher B: Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature 2000, 406:90-94.
30. Kumar R, Reynolds DM, Shevchenko A, Goldstone SD, Dalton S: Forkhead transcription factors, Fkh1p and Fkh2p, collaborate with Mcm1p to control transcription required for M-phase. Curr Biol 2000, 10:896-906.
31. McInerny CJ, Partridge JF, Mikesell GE, Creemer DP, Breeden LL: A novel Mcm1-dependent element in the SWI4, CLN3, CDC6, and CDC47 promoters activates M/G1-speciric transcription. Genes Dev 1997, 11:1277-1288.
32. Dirick L, Moll T, Auer H, Nasmyth K: A central role for SWI6 in modulating cell cycle start-specific transcription in yeast. Nature 1992, 357:508-513.
33. Ho Y, Costanzo M, Moore L, Kobayashi R, Andrews BJ: Regulation of transcription at the Saccharomyces cerevisiae start transition by Stb1, a Swi6-binding protein. Mol Cell Biol 1999, 19:5267-5278.
34. Loy CJ, Lydall D, Surana U: Ndd1, a high-dosage suppressor of cdc28-1N, is essential for expression of a subset of late-S-phase-specific genes in Saccharomyces cerevisiae. Mol Cell Biol 1999, 19:3312-3327.
35. Lim FL, Hayes A, West AG, Pic-Taylor A, Darieva Z, Morgan BA, Oliver SG, Sharrocks AD: Mcm1p-induced DNA bending regulates the formation of ternary transcription factor complexes. Mol Cell Biol 2003, 23:450-461.
36. Beer MA, Tavazoie S: Predicting gene expression from sequence. Cell 2004, 117:185-198.
37. Yeast Cell Cycle Analysis Project [http://cellcycle-www.stanford.edu/].
38. McBride HJ, Yu Y, Stillman DJ: Distinct regions of the Swi5 and Ace2 transcription factors are required for specific gene activation. J Biol Chem 1999, 274:21029-21036.
39. Cross FR, Hoek M, McKinney JD, Tinkelenberg AH: Role of Swi4 in cell cycle regulation of CLN2 expression. Mol Cell Biol 1994,14:4779-4787.
40. Costanzo M, Schub O, Andrews B: G1 Transcription factors are differentially regulated in Saccharomyces cerevisiae by the Swi6-binding protein Stb1. Mol Cell Biol 2003, 23:5064-5077.