Overview of chemical genomics and proteomics

Methods in Molecular Biology

Volumn 800, Issue , 2012, Pages 3-10

  Zanders, Edward D ^a  

^a BioVillage Ltd   (United Kingdom)

Author keywords

Affinity selection; Chemical genetics; Chemical genomics; Chemical proteomics; Connectivity map; Epigenomics; Kinases

Indexed keywords

CHEMISTRY; EPIGENETICS; GENOMICS; HUMAN; METHODOLOGY; MOLECULAR LIBRARY; PROTEOMICS; REVIEW; SYNTHESIS;

EPIGENOMICS; GENOMICS; HUMANS; PROTEOMICS; SMALL MOLECULE LIBRARIES;

EID: 80555127381     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-349-3_1     Document Type: Review

References (33)

1. Leathes JB (1930) The Harveian oration on the birth of chemical biology. Br Med J 2:671-676
2. MacBeath G (2001) Chemical genomics: what will it take and who gets to play? Genome Biol doi:10.1186/gb-2001-2-6-comment 2005
3. Schreiber SL (1998) Chemical genetics resulting from a passion for synthetic organic chemistry. Bioorg Med Chem 6:1127-52 (Pubitemid 28398950)
4. Jessani N, Liu Y, Humphrey M, Cravatt BF (2002) Enzyme activity profiles of the secreted and membrane proteome that depict cancer cell invasiveness. Proc Natl Acad Sci USA 99:10335-40
5. Jeffery DA, Bogyo M (2003) Chemical proteomics and its application to drug discovery. Curr Opin Biotechnol 14:87-95 (Pubitemid 36151848)
6. Chen TF et al. (2000) A chemical genomics approach toward understanding the global functions of the target of rapamycin protein (TOR) Proc Natl Acad Sci USA 97:13227-32
7. Caron P (2005) Introduction to Chemical Genomics. In: Zanders ED (ed) Chemical Genomics, Reviews and Protocols. Humana Press, New Jersey
8. Stockwell BR (2000) Chemical genetics: ligandbased discovery of gene function. Nat Rev Genet 1:116-25
9. Rix U, Superti-Furga G (2009) Target profiling of small molecules by chemical proteomics. Nat Chem Biol 5:616-24
10. Kidd D, Liu Y, Cravatt BF (2001) Profiling serine hydrolase activities in complex proteomes. Biochemistry 40:4005-15 (Pubitemid 32280438)
11. Hughes TR et al. (2000) Functional discovery via a compendium of expression profiles. Cell 102:109-26
12. Ganter B et al. (2005) Development of a largescale chemogenomics database to improve drug candidate selection and to understand mechanisms of chemical toxicity and action. J Biotechnol 119:219-44 (Pubitemid 41253686)
13. Lamb J (2006) The connectivity map: Using Gene-Expression Signatures to Connect Small Molecules, Genes and Disease. Science 313: 1929-1935 (Pubitemid 44497995)
14. Subramanian A (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)
15. Josset L et al. (2010) Gene expression signature-based screening identifies new broadly effective influenza A antivirals. PLoS One doi:10.1371/journal.pone.0013169
16. Hassane DC et al. (2010) Chemical genomic screening reveals synergism between parthenolide and inhibitors of the PI-3 kinase and mTOR pathways. Blood 116:5983-90
17. http://www.broadinstitute.org/cmap/Accessed 15 February 2011
18. Barrero MJ, Izpisua Belmonte JC (2011) Regenerating the epigenome. EMBO Rep doi:10.1038/embor.2011.10
19. Berdasco M, Esteller M (2010) Aberrant epigenetic landscape in cancer: how cellular identity goes awry. Dev Cell 19:698-711
20. Eliseeva ED et al. (2007) Characterization of novel inhibitors of histone acetyltransferases. Mol Cancer Ther 6:2391-8 (Pubitemid 47480404)
21. M Yoshida (2009) Chemical genomics: a key to the epigenome-an interview with Minoru Yoshida. Int J Dev Biol 53: 269-74
22. Kaida D et al. (2007) Spliceostatin A targets SF3b and inhibits both splicing and nuclear retention of pre-mRNA. Nat Chem Biol 3:533-5
23. Taverna SD Cole PA (2010) Reader's block. Nature 468:1050-1051
24. Fillipakopoulos P et al. (2010) Selective inhibition of BET bromodomains. Nature 468:1067-1073
25. Nicodeme E et al. (2010) Suppression of inflammation by a synthetic histone mimic. Nature 468:1119-1123
26. Graves PR et al. (2002) Discovery of novel targets of quinoline drugs in the human purine binding proteome. Mol Pharmacol 62:1364-72 (Pubitemid 35403831)
27. Wissing J et al. (2007) Proteomics analysis of protein kinases by target class-selective prefractionation and tandem mass spectrometry. Mol Cell Proteomics 6:537-47 (Pubitemid 46554547)
28. Bantscheff M et al. (2007) Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat Biotechnol 25:1035-44 (Pubitemid 47517638)
29. Peters EC, Gray NS (2007) Chemical Proteomics Identifies Unanticipated Targets of Clinical Kinase Inhibitors. ACS Chemical Biology 2:661-664 (Pubitemid 350066014)
30. Rix U et al. (2010) A comprehensive target selectivity survey of the BCR-ABL kinase inhibitor INNO-406 by kinase profiling and chemical proteomics in chronic myeloid leukemia cells INNO-406 target profile in CML. Leukemia 24:44-50
31. Ito T et al. (2010) Identification of a Primary Target of Thalidomide Teratogenicity. Science 327:1345-1350
32. Sakamoto S et al. (2009) Development and application of high-performance affinity beads: Toward chemical biology and drug discovery. The Chemical Record 9:66-85
33. http://www.ncgc.nih.gov/index.html Accessed 16 February 2011