Inferring Mechanisms of Compensation from E-MAP and SGA Data Using Local Search Algorithms for Max Cut

Leiserson, M., Tatar, D., Cowen, L., and Hescott, B. (2010)

Department of Computer Science, Tufts University

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Cite: M. Leiserson, D. Tatar, L. Cowen and B. Hescott, "Inferring Mechanisms of Compensation from E-MAP and SGA Data Using Local Search Algorithms for Max Cut," Recomb 2011, pp. 154-167.


BPMs & Modules
Local Cut: BPMs | Modules | Show Info
Imputed: BPMs | Modules | Show Info
Boone (Collins Genes): BPMs | Modules | Show Info
Boone (All Genes): BPMs | Modules | Show Info
Fiedler: BPMs | Modules | Show Info
Roguev: BPMs | Modules | Show Info

Datasets Used

Genetic Interactions
ChromBio E-MAP: Download | Reference: [ 4 ]
Imputed ChromBio E-MAP: Download | Reference: [ 5 ]
MAP-K E-MAP: Download | Reference: [ 6 ]
S. Pombe E-MAP: Download | Reference: [ 7 ]
Boone SGA: Download | Reference: [ 8 ]
Physical Interactions
BioGRID: Download | Show Info | Reference: [ 9 ]
Ulitsky et al.: Download | Show Info | Reference: [ 1 ]
Expression Data
Hibbs et al.: Download | Show Info | Reference: [ 10 ]


  1. Ulitsky, I., Shlomi, T., Kupiec, M., Shamir, R.: From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions. Mol. Syst. Biol. 4 (July 2008). View
  2. Bandyopadhyay, S., Kelley, R., Krogan, N.J., Ideker, T.: Functional maps of protein complexes from quantitative genetic interaction data. PLoS Comput. Biol. 4(4), e1000065 (2008). View
  3. Kelley, D., Kingsford, C.: Extracting Between-Pathway Models from E-MAP Interactions Using Expected Graph Compression. To appear in RECOMB 2010 (2010). View
  4. Collins, S.R., Miller, K.M., Maas, N.L., et al.: Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 446(7137), 806–810 (2007). View
  5. Ulitsky I, Krogan NJ, Shamir R (2009) Towards accurate imputation of quantitative genetic interactions. Genome Biol 10: R140. View
  6. Fiedler D., Braberg H., Mehta M., Chechik G., Cagney G., Mukherjee P., Silva A. C., Shales M., Collins S. R., van Wageningen S., Kemmeren P., Holstege F. C. P., Weissman J. S., Christopher-Keogh M., Koller D., Shokat K. M., Krogan N. J. (2009) Functional organization of the S. cerevisiae phosphorylation network. Cell 136, 952– 963. View
  7. A. Roguev, S. Bandyopadhyay, M. Zofall, K. Zhang, T. Fischer, S.R. Collins, H. Qu, M. Shales, H.-O. Park and J. Hayles et al., Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast, Science 322 (2008), pp. 405–410. View
  8. Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JLY, Toufighi K, Mostafavi S et al: The genetic landscape of a cell. Science 2010, 327(5964):425-431. View
  9. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. Biogrid: A General Repository for Interaction Datasets. Nucleic Acids Res. Jan1; 34:D535-9. Visit the Repository
  10. Hibbs, M.A., Hess, D.C., Myers, C.L., Huttenhower, C., Li, K., Troyanskaya, O.G.: Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinformatics 23(20), 2692–2699 (2007). View