NetwoRx: Connecting drugs to networks and phenotypes in Saccharomyces cerevisiae

Nucleic Acids Research

Volumn 41, Issue D1, 2013, Pages

  Fortney, Kristen ^a,d   Xie, Wing ^b   Kotlyar, Max ^b   Griesman, Joshua ^b   Kotseruba, Yulia ^b,e   Jurisica, Igor ^a,b,c  

^a UNIVERSITY OF TORONTO   (Canada)

^b PRINCESS MARGARET HOSPITAL   (Canada)

^c UNIVERSITY OF TORONTO   (Canada)

^d STANFORD UNIVERSITY   (United States)

^e YORK UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CISPLATIN; NEUROLEPTIC AGENT; PSYCHOTROPIC AGENT; SEDATIVE AGENT;

AGING; ARTICLE; AUTOANALYSIS; DATA EXTRACTION; DELETION MUTANT; DNA DAMAGE; DRUG MECHANISM; DRUG RESEARCH; FACTUAL DATABASE; FUNGAL GENE; FUNGAL GENOME; GENE DELETION; GENE TARGETING; GENETIC ASSOCIATION; HOMOLOGOUS RECOMBINATION; LIFESPAN; LONGEVITY; MISMATCH REPAIR; OXIDATIVE STRESS; PHENOTYPE; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE;

DATABASES, GENETIC; DNA DAMAGE; DRUG DISCOVERY; GENE REGULATORY NETWORKS; GENES, FUNGAL; HIGH-THROUGHPUT SCREENING ASSAYS; INTERNET; OXIDATIVE STRESS; PHENOTYPE; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION FACTORS;

SACCHAROMYCES CEREVISIAE;

EID: 84876566428     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1106     Document Type: Article

References (42)

1. Winzeler, E.A., Shoemaker, D.D., Astromoff, A., Liang, H., Anderson, K., Andre, B., Bangham, R., Benito, R., Boeke, J.D., Bussey, H. et al. (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science, 285, 901-906.
2. Giaever, G., Chu, A.M., Ni, L., Connelly, C., Riles, L., Veronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., Andre, B. et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature, 418, 387-391.
3. Ericson, E., Gebbia, M., Heisler, L.E., Wildenhain, J., Tyers, M., Giaever, G. and Nislow, C. (2008) Off-target effects of psychoactive drugs revealed by genome-wide assays in yeast. PLoS Genet., 4, e1000151.
4. Blackman, R.K., Cheung-Ong, K., Gebbia, M., Proia, D.A., He, S., Kepros, J., Jonneaux, A., Marchetti, P., Kluza, J., Rao, P.E. et al. (2012) Mitochondrial electron transport is the cellular target of the oncology drug elesclomol. PLoS One, 7, e29798.
5. Lamb, J., Crawford, E.D., Peck, D., Modell, J.W., Blat, I.C., Wrobel, M.J., Lerner, J., Brunet, J.P., Subramanian, A., Ross, K.N. et al. (2006) The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science, 313, 1929-1935.
6. Knox, C., Law, V., Jewison, T., Liu, P., Ly, S., Frolkis, A., Pon, A., Banco, K., Mak, C., Neveu, V. et al. (2011) DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Res., 39, D1035-D1041.
7. Hecker, N., Ahmed, J., von Eichborn, J., Dunkel, M., Macha, K., Eckert, A., Gilson, M.K., Bourne, P.E. and Preissner, R. (2012) SuperTarget goes quantitative: update on drug-target interactions. Nucleic Acids Res., 40, D1113-D1117.
8. Davis, A.P., King, B.L., Mockus, S., Murphy, C.G., Saraceni-Richards, C., Rosenstein, M., Wiegers, T. and Mattingly, C.J. (2011) The comparative toxicogenomics database: update 2011. Nucleic Acids Res., 39, D1067-D1072.
9. Kuhn, M., Szklarczyk, D., Franceschini, A., von Mering, C., Jensen, L.J. and Bork, P. (2012) STITCH 3: zooming in on protein-chemical interactions. Nucleic Acids Res., 40, D876-D880.
10. Mestres, J., Gregori-Puigjane, E., Valverde, S. and Sole, R.V. (2008) Data completeness-the Achilles heel of drug-target networks. Nat. Biotechnol., 26, 983-984.
11. Hillenmeyer, M.E., Fung, E., Wildenhain, J., Pierce, S.E., Hoon, S., Lee, W., Proctor, M., St Onge, R.P., Tyers, M., Koller, D. et al. (2008) The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science, 320, 362-365.
12. Parsons, A.B., Lopez, A., Givoni, I.E., Williams, D.E., Gray, C.A., Porter, J., Chua, G., Sopko, R., Brost, R.L., Ho, C.H. et al. (2006) Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeast. Cell, 126, 611-625.
13. Hillenmeyer, M.E., Ericson, E., Davis, R.W., Nislow, C., Koller, D. and Giaever, G. (2010) Systematic analysis of genome-wide fitness data in yeast reveals novel gene function and drug action. Genome Biol., 11, R30.
14. Iorio, F., Bosotti, R., Scacheri, E., Belcastro, V., Mithbaokar, P., Ferriero, R., Murino, L., Tagliaferri, R., Brunetti-Pierri, N., Isacchi, A. et al. (2010) Discovery of drug mode of action and drug repositioning from transcriptional responses. Proc. Natl Acad. Sci. USA, 107, 14621-14626.
15. Lowe, J.A., Jones, P. and Wilson, D.M. (2010) Network biology as a new approach to drug discovery. Curr. Opin. Drug Discov. Devel., 13, 524-526.
16. The Gene Ontology Consortium. The Gene Ontology: enhancements for 2011. Nucleic Acids Res., 40, D559-D564.
17. Kanehisa, M., Goto, S., Sato, Y., Furumichi, M. and Tanabe, M. (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res., 40, D109-D114.
18. Cherry, J.M., Hong, E.L., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E.T., Christie, K.R., Costanzo, M.C., Dwight, S.S., Engel, S.R. et al. (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res., 40, D700-D705.
19. Abdulrehman, D., Monteiro, P.T., Teixeira, M.C., Mira, N.P., Lourenco, A.B., dos Santos, S.C., Cabrito, T.R., Francisco, A.P., Madeira, S.C., Aires, R.S. et al. (2011) YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface. Nucleic Acids Res., 39, D136-D140.
20. Winzeler, E.A., Shoemaker, D.D., Astromoff, A., Liang, H., Anderson, K., Andre, B., Bangham, R., Benito, R., Boeke, J.D., Bussey, H. et al. (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science, 285, 901-906.
21. Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T. et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res., 36, D480-D484.
22. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
23. Engel, S.R., Balakrishnan, R., Binkley, G., Christie, K.R., Costanzo, M.C., Dwight, S.S., Fisk, D.G., Hirschman, J.E., Hitz, B.C., Hong, E.L. et al. (2010) Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res., 38, D433-D436.
24. Teixeira, M.C., Monteiro, P., Jain, P., Tenreiro, S., Fernandes, A.R., Mira, N.P., Alenquer, M., Freitas, A.T., Oliveira, A.L. and Sa-Correia, I. (2006) The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res., 34, D446-D451.
25. Fabrizio, P., Hoon, S., Shamalnasab, M., Galbani, A., Wei, M., Giaever, G., Nislow, C. and Longo, V.D. (2010) Genome-wide screen in Saccharomyces cerevisiae identifies vacuolar protein sorting, autophagy, biosynthetic, and tRNA methylation genes involved in life span regulation. PLoS Genet., 6, e1001024.
26. Matecic, M., Smith, D.L., Pan, X., Maqani, N., Bekiranov, S., Boeke, J.D. and Smith, J.S. (2010) A microarray-based genetic screen for yeast chronological aging factors. PLoS Genet., 6, e1000921.
27. Powers, R.W. III, Kaeberlein, M., Caldwell, S.D., Kennedy, B.K. and Fields, S. (2006) Extension of chronological life span in yeast by decreased TOR pathway signaling. Genes Devel, 20, 174-184.
28. Peter Langfelder, S.H. (2012) WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics, 9, 559.
29. Brown, K.R., Otasek, D., Ali, M., McGuffin, M., Xie, W., Devani, B., van Toch, I.L. and Jurisica, I. (2009) NAViGaTOR: network analysis, visualization and graphing Toronto. Bioinformatics, 25, 3327-3329.
30. Bolton, E.E., Wang, Y., Thiessen, P.A. and Bryant, S.H. (2008) In: Wheeler, R.A. and Spellmeyer, D.C. (eds), Annual Reports in Computational Chemistry, Vol. 4. Elsevier, Amsterdam, The Netherlands, pp. 217-241.
31. Kapitzky, L., Beltrao, P., Berens, T.J., Gassner, N., Zhou, C., Wuster, A., Wu, J., Babu, M.M., Elledge, S.J., Toczyski, D. et al. (2010) Cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action. Mol. Syst. Biol., 6, 451.
32. Fortney, K. and Jurisica, I. (2011) Integrative computational biology for cancer research. Hum. Genet., 130, 465-481.
33. de Magalhaes, J.P., Curado, J. and Church, G.M. (2009) Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics, 25, 875-881.
34. Fontana, L., Partridge, L. and Longo, V.D. (2010) Extending healthy life span-from yeast to humans. Science, 328, 321-326.
35. Lee, K.S., Lee, B.S., Semnani, S., Avanesian, A., Um, C.Y., Jeon, H.J., Seong, K.M., Yu, K., Min, K.J. and Jafari, M. (2010) Curcumin extends life span, improves health span, and modulates the expression of age-associated aging genes in Drosophila melanogaster. Rejuvenation Res., 13, 561-570.
36. Moskalev, A.A. and Shaposhnikov, M.V. (2010) Pharmacological inhibition of phosphoinositide 3 and TOR kinases improves survival of Drosophila melanogaster. Rejuvenation Res., 13, 246-247.
37. Roemer, T., Davies, J., Giaever, G. and Nislow, C. (2012) Bugs, drugs and chemical genomics. Nat. Chem. Biol., 8, 46-56.
38. Smith, A.M., Ammar, R., Nislow, C. and Giaever, G. (2010) A survey of yeast genomic assays for drug and target discovery. Pharmacol Ther, 127, 156-164.
39. Kotlyar, M., Fortney, K. and Jurisica, I. (2012) Network-based characterization of drug-regulated genes, drug targets, and toxicity. Methods, 57, 499-507.
40. Auffray, C., Chen, Z. and Hood, L. (2009) Systems medicine: the future of medical genomics and healthcare. Genome Med., 1, 2.
41. O'Connell, B.C., Adamson, B., Lydeard, J.R., Sowa, M.E., Ciccia, A., Bredemeyer, A.L., Schlabach, M., Gygi, S.P., Elledge, S.J. and Harper, J.W. (2010) A genome-wide camptothecin sensitivity screen identifies a mammalian MMS22L-NFKBIL2 complex required for genomic stability. Mol. Cell, 40, 645-657.
42. Schlabach, M.R., Luo, J., Solimini, N.L., Hu, G., Xu, Q., Li, M.Z., Zhao, Z., Smogorzewska, A., Sowa, M.E., Ang, X.L. et al. (2008) Cancer proliferation gene discovery through functional genomics. Science, 319, 620-624.