Inferring mechanisms of compensation from E-MAP and SGA data using local search algorithms for max cut

Journal of Computational Biology

Volumn 18, Issue 11, 2011, Pages 1399-1409

  Leiserson, Mark D M ^a   Tatar, Diana ^a   Cowen, Lenore J ^a   Hescott, Benjamin J ^a  

^a Tufts University   (United States)

Author keywords

algorithms; combinatorics; NP completeness

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENETIC EPISTASIS; GENETICS; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES; STATISTICAL ANALYSIS;

ALGORITHMS; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; EPISTASIS, GENETIC; MODELS, GENETIC; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES;

SACCHAROMYCETALES;

EID: 80955123851     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2011.0191     Document Type: Article

References (32)

1. Adams, C., and Kamakaka, R. 1999. Chromatin assembly: biochemical identities and genetic redundancy. Curr. Opin. Genet. Dev. 9, 185-190. (Pubitemid 29158553)
2. Bandyopadhyay, S., Kelley, R., and Krogan, N. 2008. Functional maps of protein complexes from quantitative genetic interaction data. PLoS Comput. Biol. 4, e1000065.
3. Berriz, G., King, O., Bryant, B., et al. 2003. Characterizing gene sets with funcassociate. Bioinformatics 19, 2502-2504. (Pubitemid 38016661)
4. Boone, C., Bussey, H., and Andrews, B. J. 2007. Exploring genetic interactions and networks with yeast. Nat. Rev. Genet. 8, 437-449. (Pubitemid 46789246)
5. Brady, A., Maxwell, K., Daniels, N., et al. 2009. Fault tolerance in protein interaction networks: stable bipartite subgraphs and redundant pathways. PLoS ONE 4, e5364.
6. Callebaut, I., and Mornon, J.-P. 1997. From BRCA1 to RAP1: a widespread BRCT module closely associated with DNA repair. FEBS Lett. 400, 25-30. (Pubitemid 27046815)
7. Carr, A. M. 2002. DNA structure dependent checkpoints as regulators of DNA repair. DNA Repair 1, 983-994. (Pubitemid 35335824)
8. Collins, S., Miller, K., Maas, N., et al. 2007. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 446, 806-810. (Pubitemid 46582025)
9. Costanzo, M., Baryshnikova, A., Bellay, J., et al. 2010. The genetic landscape of a cell. Science 327, 425-431.
10. D'Amours, D., and Jackson, S. 2002. The MRE11 complex: at the crossroads of DNA repair and checkpoint signalling. Nat. Rev. Mol. Cell Biol. 3, 317-327. (Pubitemid 34619266)
11. Fiedler, D., Braberg, H., Mehta, M., et al. 2009. Functional organization of the S. cerevisiae phosphorylation network. Cell 136, 952-963.
12. Green, E., Antcsak, A., Bailey, A., et al. 2005. Replication-independent histone deposition by the HIR complex and asf1. Curr. Biol. 15, 2044-2049. (Pubitemid 41654629)
13. Hescott, B. J., Leiserson, M. D. M., Slonim, D. K., et al. 2010. Evaluating between-pathway models with expression data. J. Comput. Biol. 17, 477-487.
14. Jaccard, P. 1908. Nouvelles recherches sur la distribution florale. Bull. Soc. Vaudoise Sci. Nat. 44, 223-270.
15. Jaimovich, A., Rinott, R., Schuldiner, M., et al. 2010. Modularity and directionality in genetic interaction maps. Bioinformatics 26, i228-i236.
16. Kelley, D., and Kingsford, C. 2011. Extracting between-pathway models from E-MAP interactions using expected graph compression. J. Comput. Biol. 18, 379-390.
17. Kelley, R., and Ideker, T. 2005. Systematic interpretation of genetic interactions using protein networks. Nat. Biotechnol. 23, 561-566. (Pubitemid 41724894)
18. Krogan, N., Keogh, M.-C., Datta, N., et al. 2003. A Snf2 family ATPase complex required for the recruitment of the histone H2A variant Htz1. Mol. Cell 12, 1565-1576. (Pubitemid 38037023)
19. Loebl, M. 1991. Efficient maximal cubic graph cuts. Proc. 18th Int. Colloq. Autom. Lang. Programming (ICALP) 510, 351-362.
20. Ma, X., Tarone, A. M., and Li, W. 2008. Mapping genetically compensatory pathways from synthetic lethal interactions in yeast. PLoS One 3, e1922.
21. Pan, X., Ye, P., Tuan, D., et al. 2006. A DNA integrity network in the yeast Saccharomyces cerevisiae. Cell 124, 1069-1081. (Pubitemid 43344244)
22. Poljak, S. 1995. Integer linear programs and local search for max-cut. SIAM J. Comput. 24, 822-839.
23. Real, R., and Vargas, J. 1996. The probabilistic basis of Jaccard's index of similarity. Syst. Biol. 45, 380-385. (Pubitemid 126346362)
24. Roguev, A., Bandyopadhyay, S., Zofall, M., et al. 2008. Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science 322, 405-410.
25. Schäffer, A., and Yannakakis, M. 1991. Simple local search problems that are hard to solve. SIAM J. Comput. 20, 56-87.
26. Schuldiner, M., Collins, S. R., Thompson, N. J., et al. 2005. Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell 123, 507-519. (Pubitemid 41546679)
27. Stark, C., Breitkreutz, B.-J., Reguly, T., et al. 2005. BioGRID: a general repository for interaction datasets. Nucleic Acids Res. 34, D535-D539.
28. Taipale, M., Jarosz, D., and Lindquist, S. 2010. HSP90 at the hub of protein homeostasis: emerging mechanistic insights. Nat. Rev. Mol. Cell Biol. 11, 515-528.
29. Tong, A. H. Y., Lesage, G., Bader, G. D., et al. 2004. Global Mapping of the Yeast Genetic Interaction Network. Science 303, 808-813. (Pubitemid 38174652)
30. Ulitsky, I., and Shamir, R. 2007. Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks. Mol. Syst. Biol. 3, 104.
31. Ulitsky, I., Shlomi, T., Kupiec, M., et al. 2008. From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions. Mol. Syst. Biol. 4, 209.
32. Ulitsky, I., Krogan, N., and Shamir, R. 2009. Towards accurate imputation of quantitative genetic interactions. Genome Biol. 10, R140.