Evaluating between-pathway models with expression data

Journal of Computational Biology

Volumn 17, Issue 3, 2010, Pages 477-487

  Hescott, B J ^a   Leiserson, M D M ^a   Cowen, L J ^a   Slonim, D K ^a  

^a Tufts University   (United States)

Author keywords

Combinatories; Lgorithms; NP completeness

Indexed keywords

BIOLOGICAL MODEL; CLUSTER ANALYSIS; CONFERENCE PAPER; GENE DELETION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE INACTIVATION; GENETICS; METABOLISM; REPRODUCIBILITY; SACCHAROMYCES CEREVISIAE;

CLUSTER ANALYSIS; GENE DELETION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; GENE KNOCKOUT TECHNIQUES; METABOLIC NETWORKS AND PATHWAYS; MODELS, GENETIC; REPRODUCIBILITY OF RESULTS; SACCHAROMYCES CEREVISIAE;

EID: 77950801030     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2009.0178     Document Type: Conference Paper

References (19)

1. Alam Bhuiyan, M.S., Eckstein, J., Barbuch, R., et al. 2007. Synthetically lethal interactions involving loss of the yeast erg24: the sterol c-14 reductase gene. Lipids 42, 69-76. (Pubitemid 46490745)
2. Brady, A., Maxwell, K., Daniels, N., et al. 2009. Fault tolerance in protein interaction networks: stable bipartite subgraphs and redundant pathways. PLoS One 4(4) e5364, doi: 10.1371.
3. Davidson, E.H., Rast, J.P., Oliveri, P., et al. 2002. A genomic regulatory network for development. Science 295, 1669-1678. (Pubitemid 34202895)
4. Goto, S., Bono, H., Ogata, H., et al. 1997. Organizing and computing metabolic pathway data in terms of binary relations. Pac. Symp. Biocomput. PMID: 9390290.
5. Hescott, B.J., Leiserson, M.D.M., Cowen, L., et al. 2009. Evaluating between-pathway models with expression data. Proc. RECOMB 2009.
6. Hughes, T.R., Marton, M.J., Jones, A.R., et al. 2000. Functional discovery via a compendium of expression profiles. Cell 102, 109-126.
7. Ideker, T., Ozier, O., Schwikowski, B., et al. 2002. Discovering regulatory and signaling circuits in molecular interaction networks. Bioinformatics 18, S233. (Pubitemid 41185658)
8. Kelley, R., and Ideker, T. 2005. Systematic interpretation of genetic interactions using protein networks. Nat. Biotechnol. 23, 561-566. (Pubitemid 41724894)
9. Liu, M., Liberzon, A., Kong, S.W., et al. 2007. Network-based analysis of affected biological processes in type 2 diabetes models. PLoS Genet. 3, e96. (Pubitemid 47015856)
10. Lupetti, A., Danesi, R., Campa, M., et al. 2002. Molecular basis of resistance to azole antifungals. Trends Mol. Med. 8, 76-81. (Pubitemid 34094443)
11. Ma, X., Tarone, A.M., and Li, W. 2008. Mapping genetically compensatory pathways from synthetic lethal interactions in yeast. PLoS One 3, e1922. (Pubitemid 351984123)
12. Parks, L.W., and Casey, W.M. 1995. Physiological implications of sterol biosynthesis in yeast. Annu. Rev. Microbiol. 49, 95-116.
13. Paultauf, F., Kohlwein, S., and Henry, S.A. 1992. Regulation and compartmentalization of lipid synthesis in yeast, 415-500. In: The Molecular and Cellular Biology of the Yeast Saccharomyces: Gene Expression, Volume 2.
14. Segal, E., Wang, H., and Koller, D. 2003. Discovering molecular pathways from protein interaction and gene expression data. Bioinformatics 19, Suppl 1, 264-271. (Pubitemid 41185630)
15. Subramanian, A., Tamayo, P., Mootha, V.K., et al. 2005. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545-15550. (Pubitemid 41528093)
16. Ulitsky, I., Karp, R.M., and Shamir, R. 2008. Detecting disease-specific disregulated pathways via analysis of clinical expression profiles. Proc. RECOMB 2008.
17. Ulitsky, I., and Shamir, R. 2007a. Identification of functional modules using network topology and high-throughput data. BMC Syst. Biol. 1, 8.
18. Ulitsky, I., and Shamir, R. 2007b. Pathway redundancy and protein essentiality revealed in the S. cerevisiae interaction networks. Mol. Syst. Biol. 3, 104. (Pubitemid 46625178)
19. Valachovic, M., Bareither, B.M., Alam Bhuiyan, M.S., et al. 2006. Cumulative mutations affecting sterol biosynthesis in the yeast Saccharomyces cerevisiae result in synthetic lethality that is suppressed by alterations in sphingolipid profiles. Genetics 173, 1893-1908. (Pubitemid 44285671)