Chemogenomic Profiling: Understanding the Cellular Response to Drug - Systems Biology Concepts and Insights

Biology Reference

In-Depth Information

1999;285(5429):901

6. Epub 1999/08/07. PubMed PMID:

org/10.1534/genetics.109.103036 , 2009;182. PubMed PMID:

19332878; PubMed Central PMCID: PMC2691769.

[24] Li Z, Vizeacoumar FJ, Bahr S, Li J, Warringer J, Vizeacoumar FS,

et al. Systematic exploration of essential yeast gene function with

temperature-sensitive mutants. Nat Biotechnol (4):361 e 7, http://

dx.doi.org/10.1038/nbt.1832 , 2011;29. PubMed PMID: 21441928;

PubMed Central PMCID: PMC3286520.

[25] Ho CH, Magtanong L, Barker SL, Gresham D, Nishimura S,

Natarajan P, et al. A molecular barcoded yeast ORF library

enables mode-of-action analysis of bioactive compounds. Nat

Biotechnol (4):369 e 77, http://dx.doi.org/10.1038/nbt. 1534 ,

2009;27. PubMed PMID: 19349972.

[26] Parsons AB, Brost RL, Ding H, Li Z, Zhang C, Sheikh B, et al.

Integration of chemical-genetic and genetic interaction data links

bioactive compounds to cellular target pathways. Nat Biotechnol

(1):62 e 9, http://dx.doi.org/10.1038/nbt919 , 2004;22. PubMed

PMID: 14661025.

[27] Costanzo M, Baryshnikova A, Bellay J, KimY, Spear ED, Sevier CS,

et al. The genetic landscape of a cell. Science (5964):425 e 31, http://

dx.doi.org/10.1126/science.1180823 , 2010;327. PubMed PMID:

20093466.

[28] Hu Y, Bajorath J. Polypharmacology directed compound data mining:

identification of promiscuous chemotypes with different activity

profiles and comparison to approved drugs. J chem inf model

(12):2112

10436161.

[11] Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S,

et al. Functional profiling of the Saccharomyces cerevisiae

genome. Nature (6896):387 e 91, http://dx.doi.org/10.1038/

nature00935 , 2002;418. PubMed PMID: 12140549.

[12] Pierce SE, Davis RW, Nislow C, Giaever G. Genome-wide analysis

of barcoded Saccharomyces cerevisiae gene-deletion mutants in

pooled cultures. Nat Protoc 2007;2(11):2958 e 74. PubMed PMID:

18007632.

[13] Hensel M, Shea JE, Gleeson C, Jones MD, Dalton E, Holden DW.

Simultaneous identification of bacterial virulence genes by

negative selection. Science 1995;269(5222):400 e 3. PubMed

PMID: 7618105.

[14] Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW.

Parallel human genome analysis: microarray-based expression

monitoring of 1000 genes. Proc Natl Acad Sci U S A

1996;93(20):10614 e 9. PubMed PMID: 8855227; PubMed

Central PMCID: PMC38202.

[15] David L, Huber W, Granovskaia M, Toedling J, Palm CJ,

Bofkin L, et al. A high-resolution map of transcription in the yeast

genome. Proc Natl Acad Sci U S A (14):5320 e 5, http://dx.doi.

org/10.1073/pnas.0601091103 ,

2006;103.

PubMed

PMID:

16569694; PubMed Central PMCID: PMC1414796.

[16] Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X,

Fasolo J, et al. Global analysis of protein phosphorylation

in yeast. Nature (7068):679

8, http://dx.doi.org/10.1021/ci1003637 , 2010;50. PubMed

PMID: 21070069.

[29] Azzaoui K, Hamon J, Faller B, Whitebread S, Jacoby E, Bender A,

et al. Modeling promiscuity based on in vitro safety pharmacology

profiling data. Chem Med Chem (6):874 e 80, http://dx.doi.org/10.

1002/cmdc.200700036 , 2007;2. PubMed PMID: 17492703.

[30] Takigawa I, Tsuda K, Mamitsuka H. Mining significant

substructure pairs for interpreting polypharmacology in drug-

target network. PLoS One (2):e16999, http://dx.doi.org/10.1371/

journal.pone.0016999 ,

84, http://dx.doi.org/10.1038/

nature04187 , 2005;438. PubMed PMID: 16319894.

[17] Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P,

et al. Global analysis of protein activities using proteome chips.

Science (5537):2101 e 5, http://dx.doi.org/10.1126/science.

1062191 , 2001;293. PubMed PMID: 11474067.

[18] Gallego O, Betts MJ, Gvozdenovic-Jeremic J, Maeda K, Matetzki C,

Aguilar-Gurrieri C, et al. A systematic screen for protein-lipid

interactions in Saccharomyces cerevisiae. Mol Syst Biol: 430, http://

dx.doi.org/10.1038/msb.2010.87 ,

2011;6. PubMed PMID:

21373195;

PubMed Central PMCID: PMC3044142.

[31] Overington JP, Al-Lazikani B, Hopkins AL. How many drug

targets are there? Nat Rev Drug Discov (12):993 e 6, http://dx.doi.

org/10.1038/nrd2199 , 2006;5. PubMed PMID: 17139284.

[32] Hopkins AL, Groom CR. The druggable genome. Nat Rev Drug

Discov (9):727 e 30, http://dx.doi.org/10.1038/nrd892 , 2002;1.

PubMed PMID: 12209152.

[33] Swinney DC, Anthony J. How were new medicines discovered?

Nat Rev Drug Discov (7):507 e 19, http://dx.doi.org/10.1038/

nrd3480 , 2011;10. PubMed PMID: 21701501.

[34] Oprea TI, Bologa CG, Boyer S, Curpan RF, Glen RC,

Hopkins AL, et al. A crowdsourcing evaluation of the NIH

chemical probes. Nat Chem Biol (7):441 e 7, http://dx.doi.org/10.

1038/nchembio0709 e 441 , 2009;5. PubMed PMID: 19536101.

[35] Colwill K. Renewable Protein Binder Working G, Graslund S. A

roadmap to generate renewable protein binders to the human

proteome. Nat Methods (7):551

2010;6.

PubMed

PMID:

21119626; PubMed Central PMCID: PMC3010107.

[19] Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, et al.

Global mapping of the yeast genetic interaction network.

Science (5659):808 e 13, http://dx.doi.org/10.1126/science.

1091317 , 2004;303. PubMed PMID: 14764870.

[20] Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Page N,

et al. Systematic genetic analysis with ordered arrays of yeast

deletion mutants. Science (5550):2364 e 8, http://dx.doi.org/10.

1126/science.1065810 , 2001;294. PubMed PMID: 11743205.

[21] Hillenmeyer ME, Fung E, Wildenhain J, Pierce SE, Hoon S,

Lee W, et al. The chemical genomic portrait of yeast: uncovering

a phenotype for all genes. Science (5874):362 e 5, http://dx.doi.

org/10.1126/science.1150021 ,

2008;320.

PubMed

PMID:

18420932; PubMed Central PMCID: PMC2794835.

[22] Breslow DK, Cameron DM, Collins SR, Schuldiner M, Stewart-

Ornstein J, Newman HW, et al. A comprehensive strategy

enabling high-resolution functional analysis of the yeast genome.

Nat. Methods (8):711 e 8, http://dx.doi.org/10.1038/nmeth. 1234 ,

2008;5. PubMed PMID: 18622397; PubMed Central PMCID:

PMC2756093.

[23] Yan Z, Berbenetz NM, Giaever G, Nislow C. Precise gene-dose

alleles for chemical genetics. Genetics (2):623 e 6, http://dx.doi.

8. Epub 2011/05/17, http://dx.

doi.org/10.1038/nmeth. 1607 , 2011;8. PubMed PMID: 21572409.

[36] Frye SV. The art of the chemical probe. Nat Chem Biol 6(3):

159 e 61. http://dx.doi.org/nchembio.296 [pii] 1038/nchembio.296.

PubMed PMID: 20154659.

[37] Austin CP, Brady LS, Insel TR, Collins FS. NIH molecular

libraries initiative. Science (5699):1138 e 9, http://dx.doi.org/10.

1126/science.1105511 , 2004;306. PubMed PMID: 15542455.

Systems Biology Concepts and Insights

Search WWH ::

Custom Search

Home