Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  Ye, Ping ^a,b   Peyser, Brian D ^b   Spencer, Forrest A ^b   Bader, Joel S ^a,b  

^a Johns Hopkins University   (United States)

^b JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL PATHWAYS; GENETIC INTERACTION; GENETIC NETWORKS; LARGE-SCALE DATUM; PROTEIN INTERACTION; PROTEIN INTERACTION NETWORKS; PROTEIN NETWORK; TOPOLOGICAL STRUCTURE;

ACTIVE NETWORKS; GENES; PROTEINS; YEAST;

ASSOCIATION REACTIONS;

SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; COMPUTER NETWORK; CONTROLLED STUDY; CORRELATION ANALYSIS; FUNGUS GROWTH; GENE DELETION; GENE FUNCTION; GENE INTERACTION; GENE LOCATION; GENE MUTATION; GENETIC DISTANCE; GENETIC LINKAGE; LETHALITY; MATHEMATICAL COMPUTING; NONHUMAN; PHENOTYPIC VARIATION; PREDICTION; PROTEIN LOCALIZATION; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEIN SYNTHESIS; SACCHAROMYCES CEREVISIAE; YEAST CELL; GENETICS; PROTEIN ANALYSIS;

FUNGI; SACCHAROMYCES CEREVISIAE;

PROTEIN INTERACTION MAPPING; SACCHAROMYCES CEREVISIAE;

EID: 27944503536     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-270     Document Type: Article

References (31)

1. Hartman JLt, Garvik B, Hartwell L: Principles for the buffering of genetic variation. Science 2001, 291(5506):1001-1004.
2. Tucker CL, Fields S: Lethal combinations. Nat Genet 2003, 35(3):204-205.
3. Ooi SL, Shoemaker DD, Boeke JD: DNA helicase gene interaction network defined using synthetic lethality analyzed by microarray. Nat Genet 2003, 35(3):277-286.
4. Pan X, Yuan DS, Xiang D, Wang X, Sookhai-Mahadeo S, Bader JS, Hieter P, Spencer F, Boeke JD: A robust toolkit for functional profiling of the yeast genome. Mol Cell 2004, 16(3):487-496.
5. Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Page N, Robinson M, Raghibizadeh S, Hogue CW, Bussey H et al: Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 2001, 294(5550):2364-2368.
6. Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M et al: Global mapping of the yeast genetic interaction network. Science 2004, 303(5659):808-813.
7. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM et al: Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002, 415(6868):141-147.
8. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K et al: Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 2002, 415(6868):180-183.
9. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y: A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 2001, 98(8):4569-4574.
10. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P et al: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403(6770):623-627.
11. Bader GD, Hogue CW: Analyzing yeast protein-protein interaction data obtained from different sources. Nat Biotechnol 2002, 20(10):991-997.
12. Bader JS, Chaudhuri A, Rothberg JM, Chant J: Gaining confidence in high-throughput protein interaction networks. Nat Biotechnol 2004, 22(1):78-85.
13. Barabasi AL, Oltvai ZN: Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5(2):101-113.
14. Goldberg DS, Roth FP: Assessing experimentally derived interactions in a small world. Proc Natl Acad Sci U S A 2003, 100(8):4372-4376.
15. Maslov S, Sneppen K: Specificity and stability in topology of protein networks. Science 2002, 296(5569):910-913.
16. Vazquez A, Dobrin R, Sergi D, Eckmann JP, Oltvai ZN, Barabasi AL: The topological relationship between the large-scale attributes and local interaction patterns of complex networks. Proc Natl Acad Sci U S A 2004, 101(52):17940-17945.
17. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U: Network motifs: simple building blocks of complex networks. Science 2002, 298(5594):824-827.
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(5663):1538-1542.
19. Lin N, Wu B, Jansen R, Gerstein M, Zhao H: Information assessment on predicting protein-protein interactions. BMC Bioinformatics 2004, 5(1):154.
20. Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M: A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 2003, 302(5644):449-453.
21. Middendorf M, Ziv E, Adams C, Hom J, Koytcheff R, Levovitz C, Woods G, Chen L, Wiggins C: Discriminative topological features reveal biological network mechanisms. BMC Bioinformatics 2004, 5(1):181.
22. Kelley R, Ideker T: Systematic interpretation of genetic interactions using protein networks. Nat Biotechnol 2005, 23(5):561-566.
23. Ozier O, Amin N, Ideker T: Global architecture of genetic interactions on the protein network. Nat Biotechnol 2003, 21(5):490-491.
24. Wong SL, Zhang LV, Tong AH, Li Z, Goldberg DS, King OD, Lesage G, Vidal M, Andrews B, Bussey H et al: Combining biological networks to predict genetic interactions. Proc Natl Acad Sci U S A 2004, 101(44):15682-15687.
25. Ye P, Peyser BD, Pan X, Boeke JD, Spencer FA, Bader JS: Gene function prediction from congruent synthetic lethal interactions in yeast. Molecular Systems Biology 2005, In press.
26. Newman ME, Strogatz SH, Watts DJ: Random graphs with arbitrary degree distributions and their applications. Phys Rev E Stat Nonlin Soft Matter Phys 2001, 64(2 Pt 2):026118.
27. Watts DJ, Strogatz SH: Collective dynamics of 'small-world' networks. Nature 1998, 393(6684):440-442.
28. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT et al: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25(1):25-29.
29. Geissler S, Siegers K, Schiebel E: A novel protein complex promoting formation of functional alpha- and gamma-tubulin. Embo J 1998, 17(4):952-966.
30. Vainberg IE, Lewis SA, Rommelaere H, Ampe C, Vandekerckhove J, Klein HL, Cowan NJ: Prefoldin, a chaperone that delivers unfolded proteins to cytosolic chaperonin. Cell 1998, 93(5):863-873.
31. Bader JS: Greedily building protein networks with confidence. Bioinformatics 2003, 19(15):1869-1874.