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.

Results

BPMs & Modules

Local Cut:	BPMs \| Modules \| Show Info Hide Info The Local Cut BPMs were produced using the Local Cut algorithm described in the paper on the ChromBio E-MAP from [ 4 ].
Imputed:	BPMs \| Modules \| Show Info Hide Info The Imputed BPMs were produced using the Local Cut algorithm described in the paper on the imputed ChromBio E-MAP from [ 5 ].
Boone (Collins Genes):	BPMs \| Modules \| Show Info Hide Info The Boone (ChromBio Genes) BPMs were produced using the Local Cut algorithm described in the paper on the Boone Intermediate SGA from [ 6 ], but only using interactions involving the ChromBio set of genes.
Boone (All Genes):	BPMs \| Modules \| Show Info Hide Info The Boone BPMs were produced using the Local Cut algorithm described in the paper on the Boone Intermediate SGA from [ 6 ].
Fiedler:	BPMs \| Modules \| Show Info Hide Info The Fiedler BPMs were produced using the Local Cut algorithm described in the paper on the MAP-K E-MAP from [ 6 ].
Roguev:	BPMs \| Modules \| Show Info Hide Info The Roguev BPMs were produced using the Local Cut algorithm described in the paper on the S. Pombe E-MAP from [ 7 ].

Figures

Tables

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 Hide Info \| Reference: [ 9 ] These protein interactions are all the interactions in the BioGRID 3.0.66 release of BioGRID of where the experiment type was 'physical.'
Ulitsky et al.:	Download \| Show Info Hide Info \| Reference: [ 1 ] These protein interactions were downloaded from the supplemental figures in [ 1 ].

Expression Data

Hibbs et al.:

Download | Show Info | Reference: [ 10 ]

References

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Kelley, D., Kingsford, C.: Extracting Between-Pathway Models from E-MAP Interactions Using Expected Graph Compression. To appear in RECOMB 2010 (2010). View
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
Ulitsky I, Krogan NJ, Shamir R (2009) Towards accurate imputation of quantitative genetic interactions. Genome Biol 10: R140. View
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
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
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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
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