A novel method of transcriptional response analysis to facilitate drug repositioning for cancer therapy

Cancer Research

Volumn 72, Issue 1, 2012, Pages 33-44

  Jin, Guangxu ^a,b   Fu, Changhe ^a   Zhao, Hong ^a,b   Cui, Kemi ^a,b   Chang, Jenny ^a,b,c   Wong, Stephen T C ^a,b,c  

^a Department of Obstetrics Gynecology   (United States)

^b WEILL CORNELL MEDICAL COLLEGE   (United States)

^c HOUSTON METHODIST HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMILORIDE; BEZAFIBRATE; CLOMIFENE; DAUNORUBICIN; DOXORUBICIN; ESTRADIOL; EXEMESTANE; FULVESTRANT; IMATINIB; LETROZOLE; METHOTREXATE; PACLITAXEL; RALOXIFENE; RETINOBLASTOMA PROTEIN; SULINDAC; TAMOXIFEN; TRANSCRIPTION FACTOR E2F; VALPROIC ACID;

ACCURACY; ARTICLE; BAYES THEOREM; BREAST CANCER; CANCER CELL CULTURE; CANCER INHIBITION; CANCER THERAPY; CONCENTRATION RESPONSE; CONTROLLED STUDY; DRUG REPOSITIONING; DRUG RESPONSE; DRUG TARGETING; GENE REPRESSION; GENETIC TRANSCRIPTION; MATHEMATICAL MODEL; PREDICTION; PRIORITY JOURNAL; PROMYELOCYTIC LEUKEMIA; PROSTATE CANCER; SIGNAL TRANSDUCTION;

ANTINEOPLASTIC AGENTS; HUMANS; NEOPLASMS; TRANSCRIPTION, GENETIC;

EID: 84855381399     PISSN: 00085472     EISSN: 15387445     Source Type: Journal    
DOI: 10.1158/0008-5472.CAN-11-2333     Document Type: Article

References (32)

1. Keiser MJ, Setola V, Irwin JJ, Laggner C, Abbas AI, Hufeisen SJ, et al. Predicting new molecular targets for known drugs. Nature 2009;462: 175-81.
2. Miller MA. Chemical database techniques in drug discovery. Nat Rev Drug Discov 2002;1:220-7. (Pubitemid 37361425)
3. Campillos M, Kuhn M, Gavin AC, Jensen LJ, Bork P. Drug target identification using side-effect similarity. Science 2008;321:263-6. (Pubitemid 351989100)
4. Lamb J, Crawford ED, Peck D,Modell JW, Blat IC, Wrobel MJ, et al. The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science 2006;313:1929-35. (Pubitemid 44497995)
5. Lamb J. The Connectivity Map: a new tool for biomedical research. Nat Rev Cancer 2007;7:54-60. (Pubitemid 46020847)
6. Sirota M, Dudley JT, Kim J, Chiang AP, Morgan AA, Sweet-Cordero A, et al. Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sci Transl Med 2011;3: 96ra77.
7. Sardana D, Zhu C, Zhang M, Gudivada RC, Yang L, Jegga AG. Drug repositioning for orphan diseases. Brief Bioinform 2011;12:346-56.
8. Iorio F,BosottiR, Scacheri E,Belcastro V,Mithbaokar P, Ferriero R, et al. Discovery of drugmode of action and drug repositioning fromtranscriptional responses. Proc Natl Acad Sci U S A 2010;107:14621-6.
9. Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, Tzur D, et al. DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res 2008;36:D901-6. (Pubitemid 351149842)
10. Keiser MJ, Hert J. Off-target networks derived from ligand set similarity. Methods Mol Biol 2009;575:195-205.
11. Feyen O, Lueking A, Kowald A, Stephan C, Meyer HE, Gobel U, et al. Off-target activity of TNF-alpha inhibitors characterized by protein biochips. Anal Bioanal Chem 2008;391:1713-20.
12. Creighton CJ, Massarweh S, Huang S, Tsimelzon A, Hilsenbeck SG, Osborne CK, et al. Development of resistance to targeted therapies transforms the clinically associated molecular profile subtype of breast tumor xenografts. Cancer Res 2008;68:7493-501.
13. Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T, et al. PID: the Pathway Interaction Database. Nucleic Acids Res 2009;37: D674-9.
14. Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 2005;33:D514-7. (Pubitemid 40207927)
15. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U. Network motifs: simple building blocks of complex networks. Science 2002;298:824-7. (Pubitemid 35231534)
16. Bild AH, Yao G, Chang JT, Wang Q, Potti A, Chasse D, et al. Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature 2006;439:353-7. (Pubitemid 43128862)
17. Chang JT, Carvalho C, Mori S, Bild AH, Gatza ML, Wang Q, et al. A genomic strategy to elucidate modules of oncogenic pathway signaling networks. Mol Cell 2009;34:104-14.
18. Andrechek ER, Mori S, Rempel RE, Chang JT, Nevins JR. Patterns of cell signaling pathway activation that characterize mammary development. Development 2008;135:2403-13.
19. Andrechek ER, Cardiff RD, Chang JT, Gatza ML, Acharya CR, Potti A, et al. Genetic heterogeneity of Myc-induced mammary tumors reflecting diverse phenotypes including metastatic potential. Proc Natl Acad Sci U S A 2009;106:16387-92.
20. Izmailov A, Yager TD, Zaleski H, Darash S. Improvement of base-calling in multilane automated DNA sequencing by use of electrophoretic calibration standards, data linearization, and trace alignment. Electrophoresis 2001;22:1906-14. (Pubitemid 32621916)
21. Yildirim MA, Goh KI, Cusick ME, Barabasi AL, Vidal M. Drug-target network. Nat Biotechnol 2007;25:1119-26. (Pubitemid 47538114)
22. Jin G, Zhang S, Zhang XS, Chen L. Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast. PLoS One 2007;2:e1207.
23. Shen-Orr SS, Milo R, Mangan S, Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 2002; 31:64-8.
24. Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C, et al. IntAct-open source resource for molecular interaction data. Nucleic Acids Res 2007;35:D561-5. (Pubitemid 46056270)
25. Xenarios I, Salwinski L, Duan XJ, Higney P, KimSM, Eisenberg D. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res 2002;30: 303-5. (Pubitemid 34679570)
26. Chatr-aryamontri A, Ceol A, Palazzi LM, Nardelli G, Schneider MV, Castagnoli L, et al. MINT: the Molecular INTeraction database. Nucleic Acids Res 2007;35:D572-4. (Pubitemid 46056272)
27. Mewes HW, Frishman D, Guldener U, Mannhaupt G, Mayer K, Mokrejs M, et al. MIPS: a database for genomes and protein sequences. Nucleic Acids Res 2002;30:31-4. (Pubitemid 34679496)
28. Breitkreutz BJ, Stark C, Reguly T, Boucher L, Breitkreutz A, Livstone M, et al. The BioGRID Interaction Database: 2008 update. Nucleic Acids Res 2008;36:D637-40. (Pubitemid 351149798)
29. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 2005;102:15545-50. (Pubitemid 41528093)
30. Sherr CJ, McCormick F. The RB and p53 pathways in cancer. Cancer Cell 2002;2:103-12. (Pubitemid 41039110)
31. Holbeck SL, Collins JM, Doroshow JH. Analysis of Food and Drug Administration-approved anticancer agents in the NCI60 panel of human tumor cell lines. Mol Cancer Ther 2010;9: 1451-60.
32. Riggs BL, Hartmann LC. Selective estrogen-receptor modulators -mechanisms of action and application to clinical practice.NEngl JMed 2003;348:618-29. (Pubitemid 36210865)