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Volumn 17, Issue 1, 2016, Pages

ksRepo: A generalized platform for computational drug repositioning

Author keywords

Drug discovery; Gene expression; Prostate cancer; Repositioning

Indexed keywords

DATABASE SYSTEMS; DISEASES; GENES; UROLOGY;

EID: 84960107641     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-016-0931-y     Document Type: Article
Times cited : (44)

References (30)
  • 1
    • 84922322105 scopus 로고    scopus 로고
    • Translational bioinformatics approaches to drug development
    • Readhead B, Dudley J. Translational bioinformatics approaches to drug development. Adv Wound Care (New Rochelle). 2013;2(9):470-89.
    • (2013) Adv Wound Care (New Rochelle) , vol.2 , Issue.9 , pp. 470-489
    • Readhead, B.1    Dudley, J.2
  • 2
    • 84901357361 scopus 로고    scopus 로고
    • Toward better drug repositioning: prioritizing and integrating existing methods into efficient pipelines
    • Jin G, Wong STC. Toward better drug repositioning: prioritizing and integrating existing methods into efficient pipelines. Drug Discov Today. 2014;19(5):637-44.
    • (2014) Drug Discov Today , vol.19 , Issue.5 , pp. 637-644
    • Jin, G.1    Wong, S.T.C.2
  • 3
    • 84902357848 scopus 로고    scopus 로고
    • Recent advances in drug repositioning for the discovery of new anticancer drugs
    • Shim JS, Liu JO. Recent advances in drug repositioning for the discovery of new anticancer drugs. Int J Biol Sci. 2014;10(7):654-63.
    • (2014) Int J Biol Sci , vol.10 , Issue.7 , pp. 654-663
    • Shim, J.S.1    Liu, J.O.2
  • 4
    • 84892396862 scopus 로고    scopus 로고
    • Biomarker-guided repurposing of chemotherapeutic drugs for cancer therapy: a novel strategy in drug development
    • Stenvang J, Kümler I, Nygård SB, Smith DH, Nielsen D, Brünner N, et al. Biomarker-guided repurposing of chemotherapeutic drugs for cancer therapy: a novel strategy in drug development. Front Oncol. 2013;3:313.
    • (2013) Front Oncol , vol.3 , pp. 313
    • Stenvang, J.1    Kümler, I.2    Nygård, S.B.3    Smith, D.H.4    Nielsen, D.5    Brünner, N.6
  • 5
    • 84880432356 scopus 로고    scopus 로고
    • Identifying new small molecule anti-invasive compounds for glioma treatment
    • Munson J, Bonner M, Fried L, Hofmekler J, Arbiser J, Bellamkonda R. Identifying new small molecule anti-invasive compounds for glioma treatment. Cell Cycle. 2013;12(14):2200-9.
    • (2013) Cell Cycle , vol.12 , Issue.14 , pp. 2200-2209
    • Munson, J.1    Bonner, M.2    Fried, L.3    Hofmekler, J.4    Arbiser, J.5    Bellamkonda, R.6
  • 7
    • 84870469170 scopus 로고    scopus 로고
    • High throughput screening for drug discovery of autophagy modulators
    • Shu C-W, Liu P-F, Huang C-M. High throughput screening for drug discovery of autophagy modulators. Comb Chem High Throughput Screen. 2012;15(9):721-9.
    • (2012) Comb Chem High Throughput Screen , vol.15 , Issue.9 , pp. 721-729
    • Shu, C.-W.1    Liu, P.-F.2    Huang, C.-M.3
  • 9
    • 84876958088 scopus 로고    scopus 로고
    • Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties
    • Menden MP, Iorio F, Garnett M, McDermott U, Benes CH, Ballester PJ, et al. Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties. PLoS One. 2013;8(4), e61318.
    • (2013) PLoS One , vol.8 , Issue.4
    • Menden, M.P.1    Iorio, F.2    Garnett, M.3    McDermott, U.4    Benes, C.H.5    Ballester, P.J.6
  • 10
    • 79958754253 scopus 로고    scopus 로고
    • PREDICT: a method for inferring novel drug indications with application to personalized medicine
    • Gottlieb A, Stein GY, Ruppin E, Sharan R. PREDICT: a method for inferring novel drug indications with application to personalized medicine. Mol Syst Biol. 2011;7:496.
    • (2011) Mol Syst Biol , vol.7 , pp. 496
    • Gottlieb, A.1    Stein, G.Y.2    Ruppin, E.3    Sharan, R.4
  • 12
    • 33749335282 scopus 로고    scopus 로고
    • The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease
    • 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(5795):1929-35.
    • (2006) Science , vol.313 , Issue.5795 , pp. 1929-1935
    • Lamb, J.1    Crawford, E.D.2    Peck, D.3    Modell, J.W.4    Blat, I.C.5    Wrobel, M.J.6
  • 13
    • 84961640984 scopus 로고    scopus 로고
    • DMAP: a connectivity map database to enable identification of novel drug repositioning candidates
    • Huang H, Nguyen T, Ibrahim S, Shantharam S, Yue Z, Chen JY. DMAP: a connectivity map database to enable identification of novel drug repositioning candidates. BMC Bioinformatics. 2015;16 Suppl 13:S4.
    • (2015) BMC Bioinformatics , vol.16 , pp. S4
    • Huang, H.1    Nguyen, T.2    Ibrahim, S.3    Shantharam, S.4    Yue, Z.5    Chen, J.Y.6
  • 14
    • 84927153577 scopus 로고    scopus 로고
    • Recovering drug-induced apoptosis subnetwork from Connectivity Map data
    • Yu J, Putcha P, Silva JM. Recovering drug-induced apoptosis subnetwork from Connectivity Map data. Biomed Res Int. 2015;2015:708563.
    • (2015) Biomed Res Int , vol.2015 , pp. 708563
    • Yu, J.1    Putcha, P.2    Silva, J.M.3
  • 15
    • 84926298845 scopus 로고    scopus 로고
    • Detection and screening of small molecule agents for overcoming Sorafenib resistance of hepatocellular carcinoma: a bioinformatics study
    • Lv J, Zhu B, Zhang L, Xie Q, Zhuo W. Detection and screening of small molecule agents for overcoming Sorafenib resistance of hepatocellular carcinoma: a bioinformatics study. Int J Clin Exp Med. 2015;8(2):2317-25.
    • (2015) Int J Clin Exp Med , vol.8 , Issue.2 , pp. 2317-2325
    • Lv, J.1    Zhu, B.2    Zhang, L.3    Xie, Q.4    Zhuo, W.5
  • 16
    • 84929094344 scopus 로고    scopus 로고
    • Drug repositioning for diabetes based on "omics" data mining
    • Zhang M, Luo H, Xi Z, Rogaeva E. Drug repositioning for diabetes based on "omics" data mining. PLoS One. 2015;10(5), e0126082.
    • (2015) PLoS One , vol.10 , Issue.5
    • Zhang, M.1    Luo, H.2    Xi, Z.3    Rogaeva, E.4
  • 17
    • 84943775569 scopus 로고    scopus 로고
    • Monocyte-macrophage differentiation of acute myeloid leukemia cell lines by small molecules identified through interrogation of the Connectivity Map database
    • Manzotti G, Parenti S, Ferrari-Amorotti G, Soliera AR, Cattelani S, Montanari M, et al. Monocyte-macrophage differentiation of acute myeloid leukemia cell lines by small molecules identified through interrogation of the Connectivity Map database. Cell Cycle. 2015 Jun 23;0
    • (2015) Cell Cycle , vol.23
    • Manzotti, G.1    Parenti, S.2    Ferrari-Amorotti, G.3    Soliera, A.R.4    Cattelani, S.5    Montanari, M.6
  • 18
    • 4344561557 scopus 로고    scopus 로고
    • Gene expression alterations in prostate cancer predicting tumor aggression and preceding development of malignancy
    • Yu YP, Landsittel D, Jing L, Nelson J, Ren B, Liu L, et al. Gene expression alterations in prostate cancer predicting tumor aggression and preceding development of malignancy. J Clin Oncol. 2004;22(14):2790-9.
    • (2004) J Clin Oncol , vol.22 , Issue.14 , pp. 2790-2799
    • Yu, Y.P.1    Landsittel, D.2    Jing, L.3    Nelson, J.4    Ren, B.5    Liu, L.6
  • 19
    • 70349448674 scopus 로고    scopus 로고
    • Identification of the transcription factor single-minded homologue 2 as a potential biomarker and immunotherapy target in prostate cancer
    • Arredouani MS, Lu B, Bhasin M, Eljanne M, Yue W, Mosquera J-M, et al. Identification of the transcription factor single-minded homologue 2 as a potential biomarker and immunotherapy target in prostate cancer. Clin Cancer Res. 2009;15(18):5794-802.
    • (2009) Clin Cancer Res , vol.15 , Issue.18 , pp. 5794-5802
    • Arredouani, M.S.1    Lu, B.2    Bhasin, M.3    Eljanne, M.4    Yue, W.5    Mosquera, J.-M.6
  • 20
    • 76049088558 scopus 로고    scopus 로고
    • The ubiquitin-like molecule interferon-stimulated gene 15 is overexpressed in human prostate cancer
    • Satake H, Tamura K, Furihata M, Anchi T, Sakoda H, Kawada C, et al. The ubiquitin-like molecule interferon-stimulated gene 15 is overexpressed in human prostate cancer. Oncol Rep. 2010;23(1):11-6.
    • (2010) Oncol Rep , vol.23 , Issue.1 , pp. 11-16
    • Satake, H.1    Tamura, K.2    Furihata, M.3    Anchi, T.4    Sakoda, H.5    Kawada, C.6
  • 21
    • 55349130961 scopus 로고    scopus 로고
    • DNA hypomethylation arises later in prostate cancer progression than CpG island hypermethylation and contributes to metastatic tumor heterogeneity
    • Yegnasubramanian S, Haffner MC, Zhang Y, Gurel B, Cornish TC, Wu Z, et al. DNA hypomethylation arises later in prostate cancer progression than CpG island hypermethylation and contributes to metastatic tumor heterogeneity. Cancer Res. 2008;68(21):8954-67.
    • (2008) Cancer Res , vol.68 , Issue.21 , pp. 8954-8967
    • Yegnasubramanian, S.1    Haffner, M.C.2    Zhang, Y.3    Gurel, B.4    Cornish, T.C.5    Wu, Z.6
  • 22
    • 33645123129 scopus 로고    scopus 로고
    • Epithelial-restricted gene profile of primary cultures from human prostate tumors: a molecular approach to predict clinical behavior of prostate cancer
    • Nanni S, Priolo C, Grasselli A, D'Eletto M, Merola R, Moretti F, et al. Epithelial-restricted gene profile of primary cultures from human prostate tumors: a molecular approach to predict clinical behavior of prostate cancer. Mol Cancer Res. 2006;4(2):79-92.
    • (2006) Mol Cancer Res , vol.4 , Issue.2 , pp. 79-92
    • Nanni, S.1    Priolo, C.2    Grasselli, A.3    D'Eletto, M.4    Merola, R.5    Moretti, F.6
  • 23
    • 84874271270 scopus 로고    scopus 로고
    • NCBI GEO: archive for functional genomics data sets-update
    • [Internet]. 1 [cited 2015 Jun 26]
    • Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, et al. NCBI GEO: archive for functional genomics data sets-update. Nucl Acids Res [Internet]. 2013 1 [cited 2015 Jun 26];41(D1):D991-D995.
    • (2013) Nucl Acids Res , vol.41 , Issue.D1 , pp. D991-D995
    • Barrett, T.1    Wilhite, S.E.2    Ledoux, P.3    Evangelista, C.4    Kim, I.F.5    Tomashevsky, M.6
  • 26
    • 84960148809 scopus 로고    scopus 로고
    • org.Hs.eg.db: Genome wide annotation for Human. R package version 3.1.2.
    • Carlson M. org.Hs.eg.db: Genome wide annotation for Human. R package version 3.1.2 2015.
    • (2015)
    • Carlson, M.1
  • 27
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B. 1995;57:289-300.
    • (1995) J R Stat Soc Ser B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 28
    • 33644876210 scopus 로고    scopus 로고
    • DrugBank: a comprehensive resource for in silico drug discovery and exploration
    • Wishart DS, Knox C, Guo AC, Shrivastava S, Hassanali M, Stothard P, et al. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 2006;34(Database issue):D668-72.
    • (2006) Nucleic Acids Res , vol.34 , Issue.DATABASE ISSUE , pp. D668-D672
    • Wishart, D.S.1    Knox, C.2    Guo, A.C.3    Shrivastava, S.4    Hassanali, M.5    Stothard, P.6
  • 30
    • 27744460659 scopus 로고    scopus 로고
    • PharmGKB: the pharmacogenetics and pharmacogenomics knowledge base
    • Thorn CF, Klein TE, Altman RB. PharmGKB: the pharmacogenetics and pharmacogenomics knowledge base. Methods Mol Biol. 2005;311:179-91.
    • (2005) Methods Mol Biol , vol.311 , pp. 179-191
    • Thorn, C.F.1    Klein, T.E.2    Altman, R.B.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.