Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Farkas, Illés J ^a,b   Wu, Chuang ^a   Chennubhotla, Chakra ^a   Bahar, Ivet ^a   Oltvai, Zoltán N ^a  

^a UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^b EÖTVÖS LORÁND UNIVERSITY   (Hungary)

Author keywords

[No Author keywords available]

Indexed keywords

CELLULAR FUNCTION; ENVIRONMENTAL SIGNALS; INTEGRATED RESPONSE; INTERMEDIATE LAYERS; SIGNAL INTEGRATION; SIGNAL RECOGNITION; TRANSCRIPTIONAL REGULATION; YEAST SACCHAROMYCES CEREVISIAE;

COMPLEX NETWORKS; DATA PROCESSING; TRANSCRIPTION FACTORS; YEAST;

TOPOLOGY;

TRANSCRIPTION FACTOR; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; COMPUTER PROGRAM; DATA BASE; FUNGAL GENE; GENE EXPRESSION; INFORMATION PROCESSING; NONHUMAN; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION; STIMULUS; TRANSCRIPTION REGULATION; ALGORITHM; BIOLOGICAL MODEL; COMPUTER GRAPHICS; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC DATABASE; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; MOLECULAR EVOLUTION;

SACCHAROMYCES CEREVISIAE;

ALGORITHMS; COMPUTER GRAPHICS; COMPUTER SIMULATION; DATABASES, GENETIC; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, FUNGAL; GENE REGULATORY NETWORKS; MODELS, GENETIC; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SOFTWARE; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 33751195256     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-478     Document Type: Article

References (46)

1. Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA: Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol 2004, 14:283-291.
2. Blais A, Dynlacht BD: Constructing transcriptional regulatory networks. Genes Dev 2005, 19:1499-1511.
3. Davidson EH, Erwin DH: Gene regulatory networks and the evolution of animal body plans. Science 2006, 311:796-800.
4. Svetlov VV, Cooper TG: Review: compilation and characteristics of dedicated transcription factors in Saccharomyces cerevisiae. Yeast 1995, 11:1439-1484.
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. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA: Transcriptional regulatory code of a eukaryotic genome. Nature 2004, 431:99-104.
7. Salgado H, Santos-Zavaleta A, Gama-Castro S, Peralta-Gil M, Penaloza-Spinola MI, Martinez-Antonio A, Karp PD, Collado-Vides J: The comprehensive updated regulatory network of Escherichia coli K-12. BMC Bioinformatics 2006, 7:5.
8. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U: Network motifs: simple building blocks of complex networks. Science 2002, 298:824-827.
9. Dobrin R, Beg QK, Barabasi AL, Oltvai ZN: Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network. BMC Bioinformatics 2004, 5:10.
10. Zhang LV, King OD, Wong SL, Goldberg DS, Tong AH, Lesage G, Andrews B, Bussey H, Boone C, Roth FP: Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network. J Biol 2005, 4:6.
11. Resendis-Antonio O, Freyre-Gonzalez JA, Menchaca-Mendez R, Gutierrez-Rios RM, Martinez-Antonio A, Avila-Sanchez C, Collado-Vides J: Modular analysis of the transcriptional regulatory network of E. coli. Trends Genet 2005, 21:16-20.
12. Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M: Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 2004, 431:308-312.
13. Balazsi G, Barabasi AL, Oltvai ZN: Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli. Proc Natl Acad Sci USA 2005, 102:7841-7846.
14. Erdos P, Rényi A: On the evolution of random graphs. Publ Math Inst Hung Acad Sci 1960, 5:17-61.
15. Barabasi AL, Albert R: Emergence of scaling in random networks. Science 1999, 286:509-512.
16. Guelzim N, Bottani S, Bourgine P, Kepes F: Topological and causal structure of the yeast transcriptional regulatory network. Nat Genet 2002, 31:60-63.
17. Amaral LA, Scala A, Barthelemy M, Stanley HE: Classes of small-world networks. Proc Natl Acad Sci USA 2000, 97:11149-11152.
18. Milo R, Itzkovitz S, Kashtan N, Levitt R, Shen-Orr S, Ayzenshtat I, Sheffer M, Alon U: Superfamilies of evolved and designed networks. Science 2004, 303:1538-1542.
19. Klemm K, Bornholdt S: Topology of biological networks and reliability of information processing. Proc Natl Acad Sci USA 2005, 102:18414-18419.
20. Prill RJ, Iglesias PA, Levchenko A: Dynamic properties of network motifs contribute to biological network organization. PLoS Biol 2005, 3:e343.
21. Kashtan N, Alon U: Spontaneous evolution of modularity and network motifs. Proc Natl Acad Sci USA 2005, 102:13773-13778.
22. Martin D, Brun C, Remy E, Mouren P, Thieffry D, Jacq B: GOTool-Box: functional analysis of gene datasets based on Gene Ontology. Genome Biol 2004, 5:R101.
23. 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.
24. Ambroziak J, Henry SA: INO2 and INO4 gene products, positive regulators of phospholipid biosynthesis in Saccharomyces cerevisiae, form a complex that binds to the INO1 promoter. J Biol Chem 1994, 269:15344-15349.
25. 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.
26. 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.
27. Palla G, Derenyi I, Farkas I, Vicsek T: Uncovering the overlapping community structure of complex networks in nature and society. Nature 2005, 435:814-818.
28. Garay-Arroyo A, Lledias F, Hansberg W, Covarrubias AA: Cu,Zn-superoxide dismutase of Saccharomyces cerevisiae is required for resistance to hyperosmosis. FEBS Lett 2003, 539:68-72.
29. Papin JA, Reed JL, Palsson BO: Hierarchical thinking in network biology: the unbiased modularization of biochemical networks. Trends Biochem Sci 2004, 29:641-647.
30. Yeger-Lotem E, Sattath S, Kashtan N, Itzkovitz S, Milo R, Pinter RY, Alon U, Margalit H: Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proc Natl Acad Sci USA 2004, 101:5934-5939.
31. Kiley PJ, Beinert H: Oxygen sensing by the global regulator, FNR: the role of the iron-sulfur cluster. FEMS Microbiol Rev 1998, 22:341-352.
32. Sawers G: The aerobic/anaerobic interface. Curr Opin Microbiol 1999, 2:181-187.
33. Teichmann SA, Babu MM: Gene regulatory network growth by duplication. Nat Genet 2004, 36:492-496.
34. Babu MM, Teichmann SA: Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Research 2003, 31:1234-1244.
35. Ihmels J, Bergmann S, Gerami-Nejad M, Yanai I, McClellan M, Berman J, Barkai N: Rewiring of the yeast transcriptional network through the evolution of motif usage. Science 2005, 309:938-940.
36. Kafri R, Bar-Even A, Pilpel Y: Transcription control reprogramming in genetic backup circuits. Nat Genet 2005, 37:295-299.
37. Lipan O, Wong WH: The use of oscillatory signals in the study of genetic networks. Proc Natl Acad USA 2005. 102: 7063-7068.
38. Pomerening JR, Kim SY, Ferrell JE: Systems-level dissection of the cell-cycle oscillator: bypassing positive feedback produces damped oscillations. Cell 2005, 122:565-578.
39. Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J, Guo H, Jona G, Breitkreutz A, Sopko R, McCartney RR, Schmidt MC, Rachidi N, Lee SJ, Mah AS, Meng L, Stark MJ, Stern DF, De Virgilio C, Tyers M, Andrews B, Gerstein M, Schweitzer B, Predki PF, Snyder M: Global analysis of protein phosphorylation in yeast. Nature 2005, 438:679-684.
40. Mangan S, Zaslaver A, Alon U: The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks. J Mol Biol 2003, 334:197-204.
41. Brandman O, Ferrell JE Jr, Li R, Meyer T: Interlinked fast and slow positive feedback loops drive reliable cell decisions. Science 2005, 310:496-498.
42. Guido NJ, Wang X, Adalsteinsson D, McMillen D, Hasty J, Cantor CR, Elston TC, Collins JJ: A bottom-up approach to gene regulation. Nature 2006, 439:856-860.
43. Batagelj V, Mrvar A: PAJEK - Program for large network analysis. Connections 1998, 21:47-57.
44. Wuchty S, Almaas E: Peeling the yeast protein network. Proteomics 2005, 5:444-449.
45. Adamcsek B, Palla G, Farkas IJ, Derenyi I, Vicsek T: CFinder: locating cliques and overlapping modules in biological networks. Bioinformatics 2006, 22:1021-1023.
46. Ma'ayan A, Jenkins SL, Neves S, Hasseldine A, Grace E, Dubin-Thaler B, Eungdamrong NJ, Weng G, Ram PT, Rice JJ, Kershenbaum A, Stolovitzky GA, Blitzer RD, Iyengar R: Formation of regulatory patterns during signal propagation in a Mammalian cellular network. Science 2005, 309:1078-1083.