Model of interactions in biology and application to heterogeneous network in yeast

Comptes Rendus - Biologies

Volumn 329, Issue 12, 2006, Pages 945-952

  Smidtas, Serge ^a   Yartseva, Anastasia ^b,c   Schächter, Vincent ^a   Képès, François ^d  

^a Genoscope   (France)

^b UNIVERSITÉ D EVRY VAL D ESSONNE   (France)

^c ISI FOUNDATION   (Italy)

^d University of Paris 5   (France)

Author keywords

Biological network; Formal model; Heterogeneous data

Indexed keywords

BIOINFORMATICS; BIOLOGICAL ANALYSIS; HETEROGENEOUS MEDIUM; METABOLISM; MODELING; YEAST;

ARTICLE; BIOINFORMATICS; BIOLOGY; DATA ANALYSIS; DYNAMICS; GENETIC REGULATION; HIGH THROUGHPUT SCREENING; MATHEMATICAL MODEL; METABOLISM; NONHUMAN; PROTEIN PROTEIN INTERACTION; STATISTICAL MODEL; YEAST;

EID: 33751207079     PISSN: 16310691     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.crvi.2006.06.010     Document Type: Article

References (35)

1. Goffeau A., Barrell B., Bussey H., Davis R., Dujon B., Feldmann H., Galibert F., Hoheisel J., Jacq C., Johnston M., Louis E., Mewes H., Murakami Y., Philippsen P., Tettelin H., and Oliver S. Life with 6000 genes. Science 274 5287 (1996) 546 563-567
2. Watts D., and Strogatz S. Collective dynamics of 'small-world' networks. Nature 393 6684 (1998) 440-442
3. Wagner A. The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol. Biol. Evol. 18 7 (2001) 1283-1292
4. Bader G., and Hogue C. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4 2 (2003)
5. Barabasi A., and Albert R. Emergence of scaling in random networks. Science 286 5439 (1999) 509-512
6. Schwikowski B., Uetz P., and Fields S. A network of protein-protein interactions in yeast. Nat. Biotechnol. 18 12 (2000) 1257-1261
7. Jeong H., Mason S., Barabási A., and Oltvai Z. Lethality and centrality in protein networks. Nature 411 6833 (2001) 41-42
8. Snel B., Bork P., and Huynen M. The identification of functional modules from the genomic association of genes. Proc. Natl Acad. Sci. USA 99 9 (2002) 5890-5895
9. Vazquez A., Flammini A., Maritan A., and Vespignani A. Global protein function prediction from protein-protein interaction networks. Nat. Biotechnol. 21 6 (2003) 697-700
10. Herrgård M., and Palsson B. Untangling the web of functional and physical interactions in yeast. J. Biol. 4 5 (2005)
11. Zhang L., King O., Wong S., Goldberg D.S., Tong A., Lesage G., Andrews B., Bussey H., Boone C., and Roth F. Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network. J. Biol. 4 6 (2005) 10.1186/jbiol23
12. Balasubramanian R., LaFramboise T., Scholtens D., and Gentleman R. A graph-theoretic approach to testing associations between disparate sources of functional genomics data. Bioinformatics 20 18 (2004) 3353-3362
13. S. Troncale, D. Campard, J. Guespin, J.-P. Vannier, F. Tahi, Modelisation of interleukin-6 system in early hematopoiesis with hybrid functional petri nets, in: Genopole (Ed.), Modélisation de systèmes biologiques complexes dans le contexte de la génomique, Montpellier, 4-8 avril 2005
14. Doi A., Fujita S., Matsuno H., Nagasaki M., and Miyano S. Constructing biological pathway models with hybrid functional Petri nets. In Silico Biol. 4 0023 (2004)
15. H. Matsuno, A. Doi, M. Nagasaki, S. Miyano, Hybrid petri net representation of gene regulatory network, in: Pac. Symp. Biocomput. 2000, pp. 341-352
16. de Jong H. Modeling and simulation of genetic regulatory systems: a literature review. J. Comput. Biol. 9 1 (2002) 67-103
17. Ross D., and Schoman A. Structured analysis for requirements definition. Requirements analysis. IEEE Trans. Softw. Eng. 3 1 (1977) 6-15 (special issue)
18. Louzoun Y., Solomon S., Atlan H., and Cohen I. The emergence of spatial complexity in the immune system. Physica A 297 1-2 (2001) 242-252
19. S. Smidtas, V. Schächter, F. Képès, The adaptive filter of the yeast galactose pathway, J. Theor. Biol. (in press), doi:10.1016/j.jtbi.2006.03.005
20. Ito T., Chiba T., Ozawa R., Yoshida M., Hattori M., and Sakaki Y. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA 98 8 (2001) 1569-1574
21. Uetz P., Giot L., Cagney G., Mansfield T., Judson R., Knight J., Lockshon D., Narayan V., Srinivasan M., Pochart P., Qureshi-Emili A., Li Y., Godwin B., Conover D., Kalbfleisch T., Vijayadamodar G., Yang M., Johnston M., Fields S., and Rothberg J. A comprehensive analysis of protein-protein interactions in saccharomyces cerevisiae. Nature 403 6770 (2000) 623-627
22. Ho Y., Gruhler A., Heilbut A., Bader G., Moore L., Adams S., Millar A., Taylor P., Bennett K., Boutilier K., Yang L., Wolting C., Donaldson I., Schandorff S., Shewnarane J., Vo M., Taggart J., Goudreault M., Muskat B., Alfarano C., Dewar D., Lin Z., Michalickova K., Willems A., Sassi H., Nielsen P., Rasmussen K., Andersen J., Johansen L., Hansen L., Jespersen H., Podtelejnikov A., Nielsen E., Crawford J., Poulsen V., Sørensen B., Matthiesen J., Hendrickson R., Gleeson F., Pawson T., Moran M., Durocher D., Mann M., Hogue C., Figeys D., and Tyers M. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415 6868 (2002) 180-183
23. Gavin A., Bösche M., Krause R., Grandi P., Marzioch M., Bauer A., Schultz J., Rick J., Michon A., Cruciat C., Remor M., Höfert C., Schelder M., Brajenovic M., Ruffner H., Merino A., Klein K., Hudak M., Dickson D., Rudi T., Gnau V., Bauch A., Bastuck S., Huhse B., Leutwein C., Heurtier M., Copley R., Edelmann A., Querfurth E., Rybin V., Drewes G., Raida M., Bouwmeester T., Bork P., Seraphin B., Kuster B., Neubauer G., and Superti-Furga G. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415 6868 (2002) 141-147
24. http://mips.gsf.de/proj/yeast/catalogues/complexes/
25. Guelzim N., Bottani S., Bourgine P., and Képès F. Topological and causal structure of the yeast transcriptional regulatory network. Nat. Genet. 31 1 (2002) 60-63
26. Lee T., Rinaldi N., Robert F., Odom D., Bar-Joseph Z., Gerber G., Hannett N., Harbison C., Thompson C., Simon I., Zeitlinger J., Jennings E., Murray H., Gordon D., Ren B., Wyrick J., Tagne J., Volkert T., Fraenkel E., Gifford D., and Young R. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298 5594 (2002) 799-804
27. von Mering C., Krause R., Snel B., Cornell M., Oliver S., Fields S., and Bork P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417 6887 (2002) 399-403
28. http://www.biocyc.com
29. Maziere P., Granier C., and Molina F. A description scheme of biological processes based on elementary bricks of action. J. Mol. Biol. 339 1 (2004) 77-88
30. van Helden J., Nairn A., Lemer C., Mancuso R., Eldridge M., and Wodak S. From molecular activities and processes to biological function. Briefings in Bioinformatics 2 1 (2001) 81-93
31. Shen-Orr S., Milo R., Mangan S., and Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 31 1 (2002) 64-68
32. Bardwell L., Cook J., Zhu-Shimoni J., Voora D., and Thorner J. Differential regulation of transcription: repression by unactivated mitogen-activated protein kinase kss1 requires the dig1 and dig2 proteins. Proc. Natl Acad. Sci. USA 95 26 (1998) 15400
33. Manke T., Bringas R., and Vingron M. Correlating protein-DNA and protein-protein interactions. J. Mol. Biol. 333 1 (2003) 75-85
34. de Lichtenberg U., Jensen L., Brunak S., and Bork P. Dynamic complex formation during the yeast cell cycle. Science 307 5710 (2005) 724-727
35. http://nemo-cyclone.sourceforge.net