Untangling the web of functional and physical interactions in yeast

Journal of Biology

Volumn 4, Issue 2, 2005, Pages

  Herrgård, Markus J ^a   Palsson, Bernhard Ø ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

COMPLEX FORMATION; GENETIC ORGANIZATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN MOTIF; SHORT SURVEY; YEAST; FUNGAL GENE; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PHYSIOLOGY; SACCHAROMYCES CEREVISIAE; SYSTEMS BIOLOGY; THEORETICAL MODEL;

GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; MODELS, THEORETICAL; SACCHAROMYCES CEREVISIAE; SYSTEMS BIOLOGY;

EID: 34248630494     PISSN: 14785854     EISSN: 14754924     Source Type: Journal    
DOI: 10.1186/jbiol26     Document Type: Short Survey

References (27)

1. Two-dimensional annotation of genomes. B Palsson, Nat Biotechnol 2004 22 1218 1219 10.1038/nbt1004-1218 15470454
2. Computational methods for transcriptional regulation. ED Siggia, Curr Opin Genet Dev 2005 15 214 221 10.1016/j.gde.2005.02.004 15797205
3. Protein interaction networks from yeast to human. P Bork LJ Jensen C von Mering AK Ramani I Lee EM Marcotte, Curr Opin Struct Biol 2004 14 292 299 10.1016/j.sbi.2004.05.003 15193308
4. From molecular to modular cell biology. LH Hartwell JJ Hopfield S Leibler AW Murray, Nature 1999 402 Suppl C47 C52 10.1038/35011540
5. Hierarchical thinking in network biology: the unbiased modularization of biochemical networks. JA Papin JL Reed BO Palsson, Trends Biochem Sci 2004 29 641 647 10.1016/j.tibs.2004.10.001 15544950
6. Robustness of cellular functions. J Stelling U Sauer Z Szallasi FJ Doyle 3rd J Doyle, Cell 2004 118 675 685 10.1016/j.cell.2004.09.008 15369668
7. Biological robustness. H Kitano, Nat Rev Genet 2004 5 826 837 10.1038/nrg1471 15520792
8. When kinases meet mathematics: the systems biology of MAPK signalling. W Kolch M Calder D Gilbert, FEBS Lett 2005 579 1891 1895 10.1016/j.febslet.2005. 02.002 15763569
9. The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis. JA Papin BO Palsson, Biophys J 2004 87 37 46 10.1529/biophysj.103.029884 15240442
10. Genome-scale models of microbial cells: evaluating the consequences of constraints. ND Price JL Reed BO Palsson, Nat Rev Microbiol 2004 2 886 897 10.1038/nrmicro1023 15494745
11. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. P Uetz L Giot G Cagney TA Mansfield RS Judson JR Knight D Lockshon V Narayan M Srinivasan P Pochart, Nature 2000 403 623 627 10.1038/35001009 10688190
12. Transcriptional regulatory code of a eukaryotic genome. CT Harbison DB Gordon TI Lee NJ Rinaldi KD Macisaac TW Danford NM Hannett JB Tagne DB Reynolds J Yoo, Nature 2004 431 99 104 10.1038/nature02800 15343339
13. Global mapping of the yeast genetic interaction network. AH Tong G Lesage GD Bader H Ding H Xu X Xin J Young GF Berriz RL Brost M Chang, Science 2004 303 808 813 10.1126/science.1091317 14764870
14. Reconciling gene expression data with known genome-scale regulatory network structures. MJ Herrgård MW Covert BO Palsson, Genome Res 2003 13 2423 2434 14559784 10.1101/gr.1330003
15. Motifs, themes and thematic maps of an integrated S. cerevisiae interaction network. LV Zhang OD King SL Wong DS Goldberg AH Tong G Lesage B Andrews H Bussey C Boone FP Roth, J Biol 2005 4 6 15982408 10.1186/jbiol23
16. Network motifs in the transcriptional regulation network of Escherichia coli. SS Shen-Orr R Milo S Mangan U Alon, Nat Genet 2002 31 64 68 10.1038/ng881 11967538
17. Network motifs: simple building blocks of complex networks. R Milo S Shen-Orr S Itzkovitz N Kashtan D Chklovskii U Alon, Science 2002 298 824 827 10.1126/science.298.5594.824 12399590
18. Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network. R Dobrin QK Beg AL Barabasi ZN Oltvai, BMC Bioinformatics 2004 5 10 15018656 10.1186/1471-2105-5-10
19. Systematic genetic analysis with ordered arrays of yeast deletion mutants. AH Tong M Evangelista AB Parsons H Xu GD Bader N Page M Robinson S Raghibizadeh CW Hogue H Bussey, Science 2001 294 2364 2368 10.1126/science. 1065810 11743205
20. Combining biological networks to predict genetic interactions. SL Wong LV Zhang AH Tong Z Li DS Goldberg OD King G Lesage M Vidal B Andrews H Bussey, Proc Natl Acad Sci USA 2004 101 15682 15687 15496468 10.1073/pnas.0406614101
21. DNA helicase gene interaction network defined using synthetic lethality analyzed by microarray. SL Ooi DD Shoemaker JD Boeke, Nat Genet 2003 35 277 286 10.1038/ng1258 14566339
22. Modular epistasis in yeast metabolism. D Segre A DeLuna GM Church R Kishony, Nat Genet 2005 37 77 83 15592468
23. Systematic interpretation of genetic interactions using protein networks. R Kelley T Ideker, Nat Biotechnol 2005 23 561 566 10.1038/nbt1096 15877074
24. The KEGG resource for deciphering the genome. M Kanehisa S Goto S Kawashima Y Okuno M Hattori, Nucleic Acids Res 2004 32 Database issue D277 D280 14681412 10.1093/nar/gkh063
25. Flux coupling analysis of genome-scale metabolic network reconstructions. AP Burgard EV Nikolaev CH Schilling CD Maranas, Genome Res 2004 14 301 312 14718379 10.1101/gr.1926504
26. Genomic analysis of regulatory network dynamics reveals large topological changes. NM Luscombe MM Babu H Yu M Snyder SA Teichmann M Gerstein, Nature 2004 431 308 312 10.1038/nature02782 15372033
27. Dynamic complex formation during the yeast cell cycle. U de Lichtenberg LJ Jensen S Brunak P Bork, Science 2005 307 724 727 10.1126/science.1105103 15692050