Inference of protein complex activities from chemical-genetic profile and its applications: Predicting drug-target pathways

PLoS Computational Biology

Volumn 4, Issue 8, 2008, Pages

  Han, Sangjo ^a   Kim, Dongsup ^a  

^a Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

INDICATORS (CHEMICAL); MICROCOMPUTERS; PROTEINS; YEAST;

CHEMICAL GENETICS; COMMONMODE; COMPLEX ACTIVITY; DRUG TARGETS; GROWTH DEFECTS; ITS APPLICATIONS; PROTEIN COMPLEXES; QUANTITATIVE VALUES; STRAIN GROWTHS; TARGET PROTEINS;

FORECASTING;

PROTEIN; TARGET OF RAPAMYCIN KINASE; BIOLOGICAL FACTOR; DRUG; FUNGAL PROTEIN; MULTIPROTEIN COMPLEX; PHOSPHATIDYLINOSITOL 3 KINASE; RAPAMYCIN; SACCHAROMYCES CEREVISIAE PROTEIN; TOR1 PROTEIN, S CEREVISIAE; UNCLASSIFIED DRUG;

ARTICLE; BAYES THEOREM; CELL GROWTH; CHEMICAL GENETICS; CLUSTER ANALYSIS; DRUG ACTIVITY; DRUG TARGETING; GENE DELETION; GENE INTERACTION; GENOME ANALYSIS; NONHUMAN; PHENOTYPE; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING; YEAST CELL; BIOTECHNOLOGY; CHEMISTRY; DRUG DESIGN; DRUG EFFECT; DRUG SCREENING; FUNGAL GENOME; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; METHODOLOGY; PHARMACOGENETICS; SACCHAROMYCES CEREVISIAE; TRANSGENIC ORGANISM;

1-PHOSPHATIDYLINOSITOL 3-KINASE; BAYES THEOREM; BIOLOGICAL FACTORS; BIOTECHNOLOGY; DRUG DESIGN; DRUG EVALUATION, PRECLINICAL; FUNGAL PROTEINS; GENE DELETION; GENOME, FUNGAL; MULTIPROTEIN COMPLEXES; ORGANISMS, GENETICALLY MODIFIED; PHARMACEUTICAL PREPARATIONS; PHARMACOGENETICS; PHENOTYPE; PROTEIN INTERACTION MAPPING; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SIROLIMUS;

EID: 50949089899     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000162     Document Type: Article

References (49)

1. Giaever G, Chu AM, Ni L, Connelly C, Riles L, et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387-391.
2. Yuan DS, Pan X, Ooi SL, Peyser BD, Spencer FA, et al. (2005) Improved microarray methods for profiling the Yeast Knockout strain collection. Nucleic Acids Res 33: e103.
3. Giaever G, Flaherty P, Kumm J, Proctor M, Nislow C, et al. (2004) Chemogenomic profiling: identifying the functional interactions of small molecules in yeast. Proc Natl Acad Sci U S A 101: 793-798.
4. Lum PY, Armour CD, Stepaniants SB, Cavet G, Wolf MK, et al. (2004) Discovering modes of action for therapeutic compounds using a genome-wide screen of yeast heterozygotes. Cell 116: 121-137.
5. Parsons AB, Lopez A, Givoni IE, Williams DE, Gray CA, et al. (2006) Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeast. Cell 126: 611-625.
6. Parsons AB, Brost RL, Ding H, Li Z, Zhang C, et al. (2004) Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways. Nat Biotechnol 22: 62-69.
7. Sturgeon CM, Kemmer D, Anderson HJ, Roberge M (2006) Yeast as a tool to uncover the cellular targets of drugs. Biotechnol J 1: 289-298.
8. Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440: 631-636.
9. Alberts B (1998) The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92: 291-294.
10. Liao JC, Boscolo R, Yang YL, Tran LM, Sabatti C, et al. (2003) Network component analysis: reconstruction of regulatory signals in biological systems. Proc Natl Acad Sci U S A 100: 15522-15527.
11. Sabatti C, James GM (2006) Bayesian sparse hidden components analysis for transcription regulation networks. Bioinformatics 22: 739-746.
12. Boulesteix AL, Strimmer K (2005) Predicting transcription factor activities from combined analysis of microarray and ChIP data: a partial least squares approach. Theor Biol Med Model 2: 23.
13. Yu T, Li KC (2005) Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics 21: 4033-4038.
14. Van den Bogert C, Muus P, Haanen C, Pennings A, Melis TE, et al. (1988) Mitochondrial biogenesis and mitochondrial activity during the progression of the cell cycle of human leukemic cells. Exp Cell Res 178: 143-153.
15. Hampsey M (1997) A review of phenotypes in Saccharomyces cerevisiae. Yeast 13: 1099-1133.
16. Saiardi A, Resnick AC, Snowman AM, Wendland B, Snyder SH (2005) Inositol pyrophosphates regulate cell death and telomere length through phosphoinositide 3-kinase-related protein kinases. Proc Natl Acad Sci U S A 102: 1911-1914.
17. Kunz J, Schneider U, Howald I, Schmidt A, Hall MN (2000) HEAT repeats mediate plasma membrane localization of Tor2p in yeast. J Biol Chem 275: 37011-37020.
18. Cardenas ME, Heitman J (1995) FKBP12-rapamycin target TOR2 is a vacuolar protein with an associated phosphatidylinositol-4 kinase activity. EMBO J 14: 5892-5907.
19. Liao C, Hu B, Arno MJ, Panaretou B (2007) Genomic screening in vivo reveals the role played by vacuolar H+ ATPase and cytosolic acidification in sensitivity to DNA-damaging agents such as cisplatin. Mol Pharmacol 71: 416-425.
20. Wang D, Lippard SJ (2005) Cellular processing of platinum anticancer drugs. Nat Rev Drug Discov 4: 307-320.
21. Chang M, Bellaoui M, Boone C, Brown GW (2002) A genome-wide screen for methyl methanesulfonate-sensitive mutants reveals genes required for S phase progression in the presence of DNA damage. Proc Natl Acad Sci U S A 99: 16934-16939.
22. Tercero JA, Longhese MP, Diffley JF (2003) A central role for DNA replication forks in checkpoint activation and response. Mol Cell 11: 1323-1336.
23. Knab AM, Fertala J, Bjornsti MA (1993) Mechanisms of camptothecin resistance in yeast DNA topoisomerase I mutants. J Biol Chem 268: 22322-22330.
24. Avemann K, Knippers R, Koller T, Sogo JM (1988) Camptothecin, a specific inhibitor of type I DNA topoisomerase, induces DNA breakage at replication forks. Mol Cell Biol 8: 3026-3034.
25. Vlahos CJ, Matter WF, Hui KY, Brown RF (1994) A specific inhibitor of phosphatidylinositol 3-kinase, 2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one (LY294002). J Biol Chem 269: 5241-5248.
26. Huang Q, Shen HM, Ong CN (2005) Emodin inhibits tumor cell migration through suppression of the phosphatidylinositol 3-kinase-Cdc42/Rac1 pathway. Cell Mol Life Sci 62: 1167-1175.
27. Yadav N, McDevitt RE, Benard S, Falco SC (1986) Single amino acid substitutions in the enzyme acetolactate synthase confer resistance to the herbicide sulfometuron methyl. Proc Natl Acad Sci U S A 83: 4418-4422.
28. Schmidt A, Hall MN, Koller A (1994) Two FK506 resistance-conferring genes in Saccharomyces cerevisiae, TAT1 and TAT2, encode amino acid permeases mediating tyrosine and tryptophan uptake. Mol Cell Biol 14: 6597-6606.
29. Heitman J, Koller A, Kunz J, Henriquez R, Schmidt A, et al. (1993) The immunosuppressant FK506 inhibits amino acid import in Saccharomyces cerevisiae. Mol Cell Biol 13: 5010-5019.
30. Didion T, Regenberg B, Jorgensen MU, Kielland-Brandt MC, Andersen HA (1998) The permease homologue Ssy1p controls the expression of amino acid and peptide transporter genes in Saccharomyces cerevisiae. Mol Microbiol 27: 643-650.
31. Ungar D, Oka T, Krieger M, Hughson FM (2006) Retrograde transport on the COG railway. Trends Cell Biol 16: 113-120.
32. Whyte JR, Munro S (2001) The Sec34/35 Golgi transport complex is related to the exocyst, defining a family of complexes involved in multiple steps of membrane traffic. Dev Cell 1: 527-537.
33. Morozova N, Liang Y, Tokarev AA, Chen SH, Cox R, et al. (2006) TRAPPII subunits are required for the specificity switch of a Ypt-Rab GEF. Nat Cell Biol 8: 1263-1269.
34. Schmid SL (1997) Clathrin-coated vesicle formation and protein sorting: an integrated process. Annu Rev Biochem 66: 511-548.
35. Xie MW, Jin F, Hwang H, Hwang S, Anand V, et al. (2005) Insights into TOR function and rapamycin response: chemical genomic profiling by using a high-density cell array method. Proc Natl Acad Sci U S A 102: 7215-7220.
36. Bjornsti MA, Houghton PJ (2004) The TOR pathway: a target for cancer therapy. Nat Rev Cancer 4: 335-348.
37. De Virgilio C, Loewith R (2006) The TOR signalling network from yeast to man. Int J Biochem Cell Biol 38: 1476-1481.
38. Pommier Y (2004) Camptothecins and topoisomerase I: a foot in the door. Targeting the genome beyond topoisomerase I with camptothecins and novel anticancer drugs: importance of DNA replication, repair and cell cycle checkpoints. Curr Med Chem Anticancer Agents 4: 429-434.
39. Zhang HF, Tomida A, Koshimizu R, Ogiso Y, Lei S, et al. (2004) Cullin 3 promotes proteasomal degradation of the topoisomerase I-DNA covalent complex. Cancer Res 64: 1114-1121.
40. Liakopoulos D, Doenges G, Matuschewski K, Jentsch S (1998) A novel protein modification pathway related to the ubiquitin system. EMBO J 17: 2208-2214.
41. Wu K, Chen A, Pan ZQ (2000) Conjugation of Nedd8 to CUL1 enhances the ability of the ROC1-CUL1 complex to promote ubiquitin polymerization. J Biol Chem 275: 32317-32324.
42. Osaka F, Saeki M, Katayama S, Aida N, Toh EA, et al. (2000) Covalent modifier NEDD8 is essential for SCF ubiquitin-ligase in fission yeast. EMBO J 19: 3475-3484.
43. Geissler S, Siegers K, Schiebel E (1998) A novel protein complex promoting formation of functional α- and γ-tubulin. EMBO J 17: 952-966.
44. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440: 637-643.
45. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, et al. (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Res 34: D535-D539.
46. R Development Core Team (2006) R: A Language and Environment for Statistical Computing: R Foundation for Statistical Computing.
47. Reich M, Ohm K, Angelo M, Tamayo P, Mesirov JP (2004) GeneCluster 2.0: an advanced toolset for bioarray analysis. Bioinformatics 20: 1797-1798.
48. Saldanha AJ (2004) Java Treeview - extensible visualization of microarray data. Bioinformatics 20: 3246-3248.
49. Ooi SL, Pan X, Peyser BD, Ye P, Meluh PB, et al. (2006) Global synthetic-lethality analysis and yeast functional profiling. Trends Genet 22: 56-63.