Uncovering signal transduction networks from high-throughput data by integer linear programming

Nucleic Acids Research

Volumn 36, Issue 9, 2008, Pages

  Zhao, Xing Ming ^a,b,c,d   Wang, Rui Sheng ^e   Chen, Luonan ^a,b,c,d,e   Aihara, Kazuyuki ^a,c  

^a JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^b INSTITUTE OF INTELLIGENT MACHINES   (China)

^c INSTITUTE OF INDUSTRIAL SCIENCE   (Japan)

^d SHANGHAI UNIVERSITY   (China)

^e OSAKA SANGYO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

MITOGEN ACTIVATED PROTEIN KINASE; FUNGAL PROTEIN; MEMBRANE PROTEIN; TRANSCRIPTION FACTOR;

ACCURACY; ALGORITHM; ARTICLE; BIOINFORMATICS; COMPUTER NETWORK; CONTROLLED STUDY; GENE EXPRESSION PROFILING; GENETIC IDENTIFICATION; HIGH THROUGHPUT SCREENING; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; SYSTEM ANALYSIS; YEAST; BIOLOGICAL MODEL; BIOLOGY; EVALUATION; METABOLISM; METHODOLOGY; PROTEIN ANALYSIS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; FUNGAL PROTEINS; GENE EXPRESSION PROFILING; MAP KINASE SIGNALING SYSTEM; MEMBRANE PROTEINS; MODELS, BIOLOGICAL; PROGRAMMING, LINEAR; PROTEIN INTERACTION MAPPING; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTORS; YEASTS;

EID: 44349093750     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn145     Document Type: Article

References (36)

1. Albert,R., DasGupta,B., Dondi,R., Kachalo,S., Sontag,E., Zelikovsky,A. and Westbrooks,K. (2007) A novel method for signal transduction network inference from indirect experimental evidence. J. Comput. Biol., 14, 927-949.
2. Li,S., Assmann,S.M. and Albert.R. (2006) Predicting essential components of signal transduction networks: A dynamic model of guard cell abscisic acid signaling. PLoS Biol.. 4, e312.
3. Zhao,X., Wang,R., Chen,L., and Aihara,K. (2008) Automatic modeling of signal pathways from protein-protein interaction networks. In Brazma,A., Miyano, S. and Akutsu, T., (eds), Proceedings of The 6th Asia Pacific Bioinformatics Conference, Vol. 6 of Serias on advances in bioinformatics and computational biology. Imperial College Press, Singapore, 287-296.
4. Scott,J., Ideker,T., Karp,R.M. and Sharan.R. (2006) Efficient algorithms for detecting signaling pathways in protein interaction networks. J. Comput. Biol., 13, 133-144.
5. Steffen,M., Petti,A., Aach,J., D'haeseleer,P. and Church,G. (2002) Automated modelling of signal transduction networks. BMC Bioinformatics, 3, 34.
6. Liu.Y. and Zhao,H. (2004) A computational approach for ordering signal transduction pathway components from genomics and proteomics data. BMC Bioinformatics, 5, 158.
7. Arga,K.Y., Önsan,Z., Kiidar,B., Ölgen,K. and Nielsen,J. (2007) Understanding signaling in yeast: Insights from network analysis. Biotechnol. Bioeng., 97:1246-1258.
8. Bebek,G. and Yang,J. (2007) Pathfinder: Minine signal transduction pathway segments from protein-protein interaction networks. BMC Bioinformatics, 8, 335.
9. Xenarios,I., Salwnski,L., Duan,X.J., Higney,P., Kim,S.M. and Eisenberg,D. (2002) Dip, the database of interacting proteins: A research tool for studying cellular networks of protein interactions. Nucleic Acids Res., 30, 303-305.
10. Deane,C.M., Salwinski,L., Xenarios,I. and Eisenberg,D. (2002) Protein interactions: Two methods tor assessment of the reliability of high throughput observations. Mol. Cell. Proteomicss, 1, 349-356.
11. Sharan,R., Suthram,S., Kelley,R.M., Kuhn,T., McCuine,S., Uetz,P., Sittler,T., Karp,R.M. and Ideker,T. (2005) From the cover: Conserved patterns of protein interaction in multiple species. Proc. Natl Acad. Sci. USA, 102, 1971-1979.
12. Daran-Lapujade,P., Jansen,M.L.A. Daran,J., van Gulik,W., de Winde,J.H. and Pronk,J.T. (2004) Role of transcriptional regulation in controlling fluxes in central carbon metabolism of saccharomyces cerevisiae: A chemostat culture study. J. Biol. Chem., 279, 9125-9138.
13. Gasch,A.P., Spellman,P.T., Kao,C.M., Carmel-Harel,O., Eisen,M.B., Storz,G., Botstein,D. and Brown,P.O. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell, 11, 4241-4257.
14. Hughes,T.R., Marton,M.J., Jones,A.R., Roberts,C.J., Stoughton,R., Armour,C.D., Bennett.H.A., Coey,E., Dai,H., He,Y.D. et al. (2000) Functional discovery via a compendium of expression profiles. Cell 102, 109-126.
15. DeRisi,J.L., Iyer,V.R. and Brown,P.O. (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science, 278, 680-686.
16. Ogawa,N., DeRisi,J. and Brown,P.O. (2000) New components of a system for phosphate accumulation and polyphosphate metabolism in saccharomyces cerevisiae revealed by genomic expression analysis. Mol. Biol. Cell 11, 4309-4321.
17. Edgar,R., Domrachev,M. and Lash,A.E. (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res., 30, 207-210.
18. Bardwell,L., Zou,X., Nie,Q. and Komarova,N.L. (2007) Mathematical models ot specificity in cell signaling. Biophys. J., 92, 3425-3441.
19. Zou,X., Chen,Y. and Pan,Z. (2006) Modeling and optimization of the specifficity in cell signaling pathways based on a high performance multi-objective evolutionary algorithm. Leet. Notes Comput. Sci., 4247, 774-781.
20. Hill,T., Lundgren,A., Fredriksson,R. and Schioth,H.B. (2005) Genetice algorithm for large-scale maximum parsimony phylogenetic analysis of proteins. Biochim. Biophys. Acta, 1725, 19-29.
21. Wang,L. and Xu,Y. (2003) Haplotype inference by maximum parsimony. Bioinformatics, 19, 1773-1780.
22. Batagelj,V., Pajek. (2007) http://vlado.fmf.uni-lj.si/pub/networks/ pajek/, access date: October, 2007.
23. Ashburner,M., Ball,C.A., Blake,J.A., Botstein,D., Butler,H., Cherry,J.M., Davis,A.P., Dolinski,K., Dwight,S.S., Eppig,J.T. et al. (2000) Gene ontology: Tool for the unification of biology. The gene ontology consortium. Nat. Genet., 25, 25-29.
24. Cherry,J.M., Adler,C., Ball,C., Chervitz,S.A. Dwight.S.S., Hester,E.T., Jia,Y., Juvik,G., Roe,T., Schroeder,M. et al. (1998) Sgd: Saccharomyces genome database. Nucleic Acids Res, 26, 73-79.
25. Kanehisa,M., Goto,S., Hattori,M., Aoki-Kinoshita,K.F., Itoh,M., Kawashima,S., Katayama,T., Araki,M. and Hirakawa,M. (2006) Nucleic Acids Res., 34(Database issue), D354-D357.
26. Oehlen,L.J. and Cross,F.R. (1994) G1 cyclins CLN1 and CLN2 repress the mating factor response pathway at Start in the yeast cell cycle. Genes Dev., 8, 1058-1070.
27. Oehlen,L.J. and Cross,F.R. (1998) Potential regulation of ste20 function by the cln1-cdc28 and cln2-cdc28 cyclin-dependent protein kinases. J. Biol. Chem., 273, 25089-25097.
28. Mewes,H.W., Amid,C., Arnold,R., Frishman,D., Gldener,U., Mannhaupt,G., Mnsterkötter,M., Pagel,P., Strack,N., Stmpflen,V. et al. (2004) Mips: Analysis and annotation of proteins from whole genomes. Nucleic Acids Res., 32(Database issue): D41-44.
29. Osman,M.A. and Cerione,R.A. (1998) Iqg1p, a yeast homologue of the mammalian iqgaps, mediates cdc42p effects on the actin cytoskeleton. J. Cell. Biol., 142, 443-455.
30. Kawasaki,R., Fujimura-Kamada,K., Toi,M., Kato,H. and Tanaka,K. (2003) The upstream regulator, Rsr1p and downstream effectors, Gic1p and Gic2p, of the Cdc42p small GTPase coordinately regulate initiation of budding in Saccharomyces cerevisiae. Genes Cells, 8, 235-250.
31. Poon,P., Wang,X., Rotman,M., Huber,I., Cukierman,E., Cassel,D., Singer,R.A. and Johnston,G.C. (1996) Saccharomyces cerevisiae Ges1 is an ADP ribosylation factor GTPase-activating protein. Proc. Natl Acad. Sci. USA, 93, 10074-10077.
32. Virag,A. and Harri,S.D. (2006) Functional characterization of aspergillus nidulans homologues of saccharomyces cerevisiae spa2 and bud6. Eukaryot. Cell, 5, 881-895.
33. Serikawa,K.A., Xu,X.L., MacKay,V.L., Law,G.L., Zong,Q., Zhao,L.P., Bumgarner,R. and Morris,D.R. (2003) The transcriptome and its translation during recovery from cell cycle arrest in saccharomyces cerevisiae. Mol. Cell. Proteomics, 2, 191-204.
34. Roemer,T., Vallier,L., Sheu,Y.J. and Snyder,M.(1998) The Spa2-related protein, Sph1p, is important for polarized growth in yeast. J. Cell Sci., 111, 479-494.
35. Helliwell,S.B., Schmidt,A., Ohya,Y. and Hall,M.N. (1998) The Rho1 effector Pkc1, but not Bni1, mediates signaling from Tor2 to the actin cytoskeleton, Curr. Biol., 8, 1211-1214.
36. Hirano,H., Tanaka,K., Ozaki,K., Imamura,H., Kohno,H., Hihara,T., Kameyama,T., Hotta,K., Arisawa,M., Watanabe,T. et al. (1996) ROM7/ BEM4 encodes a novel protein that interacts with the Rho1p small GTP-binding protein in Saccharomyces cerevisiae. Mol. Cell. Biol., 16, 4396-4403.