The polarity sub-network in the yeast network of protein-protein interactions

Network Biology

Volumn 1, Issue 3-4, 2011, Pages 149-158

  Paris, Luca ^a   Bazzoni, Gianfranco ^a  

^a MARIO NEGRI INSTITUTE FOR PHARMACOLOGICAL RESEARCH   (Italy)

Author keywords

Budding yeast; Cell polarity; Connectivity; Protein interaction networks; Protein interactions; Topological role

Indexed keywords

EID: 84865863301     PISSN: None     EISSN: 22208879     Source Type: Journal    
DOI: 10.0000/issn-2220-8879-networkbiology-2011-v1-0015     Document Type: Article

References (39)

1. Albert R, Jeong H, Barabasi AL. 2000. Error and attack tolerance of complex networks. Nature, 406: 378-382
2. Ashburner M, Ball CA, Blake JA, et al. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics, 25: 25-29
3. Barabasi AL, Albert R. 1999. Emergence of scaling in random networks. Science, 286: 509-512
4. Barabasi AL, Oltvai ZN. 2004. Network biology: understanding the cell's functional organization. Nat Rev Genet, 5: 101-113
5. Bork P, Jensen LJ, von Mering C, et al. 2004. Protein interaction networks from yeast to human. Current Opinion in Structure Biology, 14: 292-299
6. Cherry JM, Ball C, Weng S, et al. 1997. Genetic and physical maps of Saccharomyces cerevisiae. Nature, 387: 67-73
7. Cirillo N, Prime SS. 2009. Desmosomal interactome in keratinocytes: a systems biology approach leading to an understanding of the pathogenesis of skin disease. Cellular and Molecular Life Sciences, 66: 3517-3533
8. Collins SR, Kemmeren P, Zhao XC, et al. 2007. Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Molecular and Cellular Proteomics, 6: 439-450
9. de Hoon MJ, Imoto S, Nolan J, et al. 2004. Open source clustering software. Bioinformatics, 20: 1453-1454
10. Drees BL, Sundin B, Brazeau E, et al. 2001. A protein interaction map for cell polarity development. Journal of Cell Biology, 154: 549-571
11. Drubin DG, Nelson WJ. 1996. Origins of cell polarity. Cell, 84: 335-344
12. Eisen MB, Spellman PT, Brown PO, et al. 1998. Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Sciences of U. S. A., 95: 14863-14868
13. Erdös P, Rényi A. 1960. On the evolution of random graph. Publ Math Inst Hung Acad Sci, 5: 17-61
14. Evangelista M, Blundell K, Longtine MS, et al. 1997. Bni1p, a yeast formin linking cdc42p and the actin cytoskeleton during polarized morphogenesis. Science, 276: 118-122
15. Gavin AC, Aloy P, Grandi P, et al. 2006. Proteome survey reveals modularity of the yeast cell machinery. Nature, 440: 631-636
16. Goemann B, Wingender E, Potapov AP. 2011. Topological peculiarities of mammalian networks with different functionalities: transcription, signal transduction and metabolic networks. Network Biology, 1(3-4): 134-148
17. Guimera R, Nunes Amaral LA. 2005. Functional cartography of complex metabolic networks. Nature, 433: 895-900
18. Hartwell LH, Hopfield JJ, Leibler S, et al. 1999. From molecular to modular cell biology. Nature, 402: C47-52
19. Ibrahim SS, Eldeeb MAR, Rady MAH. 2011. The role of protein interaction domains in the human cancer network. Network Biology, 1(1): 59-71
20. Jain S, Bhooshan SV, Naik PK. 2011. Mathematical modeling deciphering balance between cell survival and cell death using insulin. Network Biology, 1(1): 46-58
21. Kashtan N, Alon U. 2005. Spontaneous evolution of modularity and network motifs. Proceedings of the National Academy of Sciences of U. S. A., 102: 13773-13778
22. Martínez-Antonio A. 2011. Escherichia coli transcriptional regulatory network. Network Biology, 1(1): 21-33
23. Newman ME, Girvan M. 2004. Finding and evaluating community structure in networks. Physical Review E: Statistical, Nonlinear, and Soft Matter Physics, 69: 026113
24. Paris L, Bazzoni G. 2008. The protein interaction network of the epithelial junctional complex: a system-level analysis. Molecular Biology of the Cell, 19: 5409-5421.
25. Pruyne D, Bretscher A. 2000. Polarization of cell growth in yeast. Journal of Cell Science, 113(Pt 4): 571-585
26. Pruyne D, Bretscher A. 2000. Polarization of cell growth in yeast. I. Establishment and maintenance of polarity states. Journal of Cell Science, 113 (Pt 3): 365-375
27. Rachlin J, Cohen DD, Cantor C, Kasif S. 2006. Biological context networks: a mosaic view of the interactome. Molecular Systems Biology, 2: 66
28. Ravasz E, Somera AL, Mongru DA, et al. 2002. Hierarchical organization of modularity in metabolic networks. Science, 297: 1551-1555
29. Rives AW, Galitski T. 2003. Modular organization of cellular networks. Proceedings of the National Academy of Sciences of U. S. A., 100: 1128-1133
30. Rodriguez A, Infante D. 2011. Characterization in silico of flavonoids biosynthesis in Theobroma cacao L. Network Biology, 2011, 1(1): 34-45
31. Saldanha AJ. 2004. Java Treeview--extensible visualization of microarray data. Bioinformatics, 20: 3246-3248
32. Shannon P, Markiel A, Ozier O, et al. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research, 13: 2498-2504
33. Sheu YJ, Santos B, Fortin N, et al. 1998. Spa2p interacts with cell polarity proteins and signaling components involved in yeast cell morphogenesis. Molecular and Cellular Biology, 18: 4053-4069
34. Tcheperegine SE, Gao XD, Bi E. 2005. Regulation of cell polarity by interactions of Msb3 and Msb4 with Cdc42 and polarisome components. Molecular and Cellular Biology, 25: 8567-8580
35. Tacutu R, Budovsky A, Yanai H, et al. 2011. Immunoregulatory network and cancer-associated genes: molecular links and relevance to aging. Network Biology, 1(2): 112-120
36. Vidal M, Cusick ME, Barabasi AL. 2011. Interactome networks and human disease. Cell, 144: 986-998
37. Watts DJ, Strogatz SH. 1998. Collective dynamics of 'small-world' networks. Nature, 393: 440-442
38. Zaidel-Bar R, Itzkovitz S, Ma'ayan A, et al. 2007. Functional atlas of the integrin adhesome. Nature Cell Biology, 9: 858-867
39. Zhang WJ. 2011. Constructing ecological interaction networks by correlation analysis: hints from community sampling. Network Biology, 1(2): 81-98