메뉴 건너뛰기




Volumn 18, Issue 1, 2014, Pages 34-41

Integrative gene set analysis: Application to platinum pharmacogenomics

Author keywords

[No Author keywords available]

Indexed keywords

CISPLATIN; MESSENGER RNA; SMALL INTERFERING RNA;

EID: 84893107986     PISSN: 15362310     EISSN: 15578100     Source Type: Journal    
DOI: 10.1089/omi.2013.0099     Document Type: Article
Times cited : (12)

References (46)
  • 1
    • 84865060986 scopus 로고    scopus 로고
    • Identifying the genetic variation of gene expression using gene sets: Application of novel gene set eQTL approach to PharmGKB and KEGG
    • Abo R, Jenkins GD, Wang L, and Fridley BL. (2012). Identifying the genetic variation of gene expression using gene sets: Application of novel gene set eQTL approach to PharmGKB and KEGG. PLoS One 7, e43301
    • (2012) PLoS One , vol.7
    • Abo, R.1    Jenkins, G.D.2    Wang, L.3    Fridley, B.L.4
  • 2
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology. The gene ontology consortium
    • Ashburner M, Ball CA, Blake JA, et al. (2000). Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25, 25-29
    • (2000) Nat Genet , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3
  • 3
    • 77949855319 scopus 로고    scopus 로고
    • Comparisons of multimarker association methods to detect association between a candidate region and disease
    • Ballard DH, Cho J, and Zhao H. (2010). Comparisons of multimarker association methods to detect association between a candidate region and disease. Genet Epidemiol 34, 201-212
    • (2010) Genet Epidemiol , vol.34 , pp. 201-212
    • Ballard, D.H.1    Cho, J.2    Zhao, H.3
  • 5
    • 43749122409 scopus 로고    scopus 로고
    • Prediction of metastatic relapse in node-positive breast cancer: Establishment of a clinicogenomic model after FEC100 adjuvant regimen
    • Campone M, Campion L, Roche H, et al. (2008). Prediction of metastatic relapse in node-positive breast cancer: Establishment of a clinicogenomic model after FEC100 adjuvant regimen. Breast Cancer Res Treat 109, 491-501
    • (2008) Breast Cancer Res Treat , vol.109 , pp. 491-501
    • Campone, M.1    Campion, L.2    Roche, H.3
  • 8
    • 0035148254 scopus 로고    scopus 로고
    • CENP-F gene amplification and overexpression in head and neck squamous cell carcinomas
    • De La Guardia C, Casiano CA, Trinidad-Pinedo J, and Baez A. (2001). CENP-F gene amplification and overexpression in head and neck squamous cell carcinomas. Head Neck 23, 104-112
    • (2001) Head Neck , vol.23 , pp. 104-112
    • De La Guardia, C.1    Casiano, C.A.2    Trinidad-Pinedo, J.3    Baez, A.4
  • 10
    • 80054971057 scopus 로고    scopus 로고
    • Gene set analysis of purine and pyrimidine antimetabolites cancer therapies
    • Fridley BL, Batzler A, Li L, et al. (2011). Gene set analysis of purine and pyrimidine antimetabolites cancer therapies. Pharmacogenet Genomics 21, 701-712
    • (2011) Pharmacogenet Genomics , vol.21 , pp. 701-712
    • Fridley, B.L.1    Batzler, A.2    Li, L.3
  • 11
    • 77958614226 scopus 로고    scopus 로고
    • Self-contained gene-set analysis of expression data: An evaluation of existing and novel methods
    • Fridley BL, Jenkins GD, and Biernacka JM. (2010). Self-contained gene-set analysis of expression data: An evaluation of existing and novel methods. PLoS One 5, e12693
    • (2010) PLoS One , vol.5
    • Fridley, B.L.1    Jenkins, G.D.2    Biernacka, J.M.3
  • 12
    • 84859378506 scopus 로고    scopus 로고
    • Gene set analysis of survival following ovarian cancer implicates macrolide binding and intracellular signaling genes
    • Fridley BL, Jenkins GD, Tsai YY, et al. (2012). Gene set analysis of survival following ovarian cancer implicates macrolide binding and intracellular signaling genes. Cancer Epidemiol Biomarkers Prevent 21, 529-536
    • (2012) Cancer Epidemiol Biomarkers Prevent , vol.21 , pp. 529-536
    • Fridley, B.L.1    Jenkins, G.D.2    Tsai, Y.Y.3
  • 14
    • 34447315844 scopus 로고    scopus 로고
    • Testing association between disease and multiple SNPs in a candidate gene
    • Gauderman WJ, Murcray C, Gilliland F, and Conti DV. (2007). Testing association between disease and multiple SNPs in a candidate gene. Genet Epidemiol 31, 383-395
    • (2007) Genet Epidemiol , vol.31 , pp. 383-395
    • Gauderman, W.J.1    Murcray, C.2    Gilliland, F.3    Conti, D.V.4
  • 15
    • 34249663294 scopus 로고    scopus 로고
    • Analyzing gene expression data in terms of gene sets: Methodological issues
    • Goeman JJ, and Buhlmann P. (2007). Analyzing gene expression data in terms of gene sets: Methodological issues. Bioinformatics 23, 980-987
    • (2007) Bioinformatics , vol.23 , pp. 980-987
    • Goeman, J.J.1    Buhlmann, P.2
  • 17
    • 0026689178 scopus 로고
    • Performing the exact test of Hardy-Weinberg proportion for multiple alleles
    • Guo SW, and Thompson EA. (1992). Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48, 361-372
    • (1992) Biometrics , vol.48 , pp. 361-372
    • Guo, S.W.1    Thompson, E.A.2
  • 18
    • 0036088113 scopus 로고    scopus 로고
    • Pharmgkb: The pharmacogenetics knowledge base
    • Hewett M, Oliver DE, Rubin DL, et al. (2002). PharmGKB: The Pharmacogenetics Knowledge Base. Nucleic Acids Res 30, 163-165
    • (2002) Nucleic Acids Res , vol.30 , pp. 163-165
    • Hewett, M.1    Oliver, D.E.2    Rubin, D.L.3
  • 19
    • 84862908939 scopus 로고    scopus 로고
    • Integrated analysis of multiple gene expression profiling datasets revealed novel gene signatures and molecular markers in nasopharyngeal carcinoma
    • Huang C, Tang H, Zhang W, et al. (2012). Integrated analysis of multiple gene expression profiling datasets revealed novel gene signatures and molecular markers in nasopharyngeal carcinoma. Cancer Epidemiol Biomarkers Prevent 21, 166-175
    • (2012) Cancer Epidemiol Biomarkers Prevent , vol.21 , pp. 166-175
    • Huang, C.1    Tang, H.2    Zhang, W.3
  • 20
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • Kanehisa M, and Goto S. (2000). KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28, 27-30
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 21
    • 75549090213 scopus 로고    scopus 로고
    • KEGG for representation and analysis of molecular networks involving diseases and drugs
    • Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. (2010). KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 38, D355-360
    • (2010) Nucleic Acids Res , vol.38
    • Kanehisa, M.1    Goto, S.2    Furumichi, M.3    Tanabe, M.4    Hirakawa, M.5
  • 22
    • 0035755351 scopus 로고    scopus 로고
    • Integrating genotype and phenotype information: An overview of the PharmGKB project. Pharmacogenetics research network and knowledge base
    • Klein TE, Chang JT, Cho MK, et al. (2001). Integrating genotype and phenotype information: An overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base. Pharmacogenomics J 1, 167-170
    • (2001) Pharmacogenomics J , vol.1 , pp. 167-170
    • Klein, T.E.1    Chang, J.T.2    Cho, M.K.3
  • 23
    • 33644682472 scopus 로고    scopus 로고
    • Modulation of cell cycle and gene expression in pancreatic tumor cell lines by methionine deprivation (methionine stress): Implications to the therapy of pancreatic adenocarcinoma
    • Kokkinakis DM, Liu X, and Neuner RD. (2005). Modulation of cell cycle and gene expression in pancreatic tumor cell lines by methionine deprivation (methionine stress): Implications to the therapy of pancreatic adenocarcinoma. Mol Cancer Therapeut 4, 1338-1348
    • (2005) Mol Cancer Therapeut , vol.4 , pp. 1338-1348
    • Kokkinakis, D.M.1    Liu, X.2    Neuner, R.D.3
  • 24
    • 52049100798 scopus 로고    scopus 로고
    • Gemcitabine and cytosine arabinoside cytotoxicity: Association with lymphoblastoid cell expression
    • Li L, Fridley B, Kalari K, et al. (2008). Gemcitabine and cytosine arabinoside cytotoxicity: Association with lymphoblastoid cell expression. Cancer Res 68, 7050-7058
    • (2008) Cancer Res , vol.68 , pp. 7050-7058
    • Li, L.1    Fridley, B.2    Kalari, K.3
  • 25
    • 70450189297 scopus 로고    scopus 로고
    • Gemcitabine and arabinosylcytosin pharmacogenomics: Genome-wide association and drug response biomarkers
    • Li L, Fridley BL, Kalari K, et al. (2009). Gemcitabine and arabinosylcytosin pharmacogenomics: Genome-wide association and drug response biomarkers. PLoS One 4, e7765
    • (2009) PLoS One , vol.4
    • Li, L.1    Fridley, B.L.2    Kalari, K.3
  • 26
    • 84855839425 scopus 로고    scopus 로고
    • Screening of autoantibodies as potential biomarkers for hepatocellular carcinoma by using T7 phase display system
    • Liu H, Zhang J, Wang S, et al. (2012). Screening of autoantibodies as potential biomarkers for hepatocellular carcinoma by using T7 phase display system. Cancer Epidemiol 36, 82-88
    • (2012) Cancer Epidemiol , vol.36 , pp. 82-88
    • Liu, H.1    Zhang, J.2    Wang, S.3
  • 27
    • 30744451927 scopus 로고    scopus 로고
    • Association between glutathione S-Transferase pi polymorphisms and survival in patients with advanced nonsmall cell lung carcinoma
    • Lu C, Spitz MR, Zhao H, et al. (2006). Association between glutathione S-Transferase pi polymorphisms and survival in patients with advanced nonsmall cell lung carcinoma. Cancer 106, 441-447
    • (2006) Cancer , vol.106 , pp. 441-447
    • Lu, C.1    Spitz, M.R.2    Zhao, H.3
  • 29
    • 0034107685 scopus 로고    scopus 로고
    • Role of metallothionein in cisplatin sensitivity of germ-cell tumours
    • Meijer C, Timmer A, De Vries EG, et al. (2000). Role of metallothionein in cisplatin sensitivity of germ-cell tumours. Int J Cancer 85, 777-781
    • (2000) Int J Cancer , vol.85 , pp. 777-781
    • Meijer, C.1    Timmer, A.2    De Vries, E.G.3
  • 30
    • 0032716921 scopus 로고    scopus 로고
    • Decreased and aberrant nuclear lamin expression in gastrointestinal tract neoplasms
    • Moss SF, Krivosheyev V, De Souza A, et al. (1999). Decreased and aberrant nuclear lamin expression in gastrointestinal tract neoplasms. Gut 45, 723-729
    • (1999) Gut , vol.45 , pp. 723-729
    • Moss, S.F.1    Krivosheyev, V.2    De Souza, A.3
  • 31
    • 78649300012 scopus 로고    scopus 로고
    • Radiation pharmacogenomics: A genome-wide association approach to identify radiation response biomarkers using human lymphoblastoid cell lines
    • Niu N, Qin Y, Fridley BL, et al. (2010). Radiation pharmacogenomics: A genome-wide association approach to identify radiation response biomarkers using human lymphoblastoid cell lines. Genome Res 20, 1482-1492
    • (2010) Genome Res , vol.20 , pp. 1482-1492
    • Niu, N.1    Qin, Y.2    Fridley, B.L.3
  • 32
    • 11144355405 scopus 로고    scopus 로고
    • Glutathione Stransferase polymorphisms and survival in primary malignant glioma
    • Okcu MF, Selvan M, Wang LE, et al. (2004). Glutathione Stransferase polymorphisms and survival in primary malignant glioma. Clin Cancer Res 10, 2618-2625
    • (2004) Clin Cancer Res , vol.10 , pp. 2618-2625
    • Okcu, M.F.1    Selvan, M.2    Wang, L.E.3
  • 33
    • 0033993937 scopus 로고    scopus 로고
    • Concurrent chemotherapy and pelvic radiation therapy compared with pelvic radiation therapy alone as adjuvant therapy after radical surgery in high-risk early-stage cancer of the cervix
    • Peters WA, 3rd, Liu PY, Barrett RJ, 2nd, et al. (2000). Concurrent chemotherapy and pelvic radiation therapy compared with pelvic radiation therapy alone as adjuvant therapy after radical surgery in high-risk early-stage cancer of the cervix. J Clin Oncol 18, 1606-1613
    • (2000) J Clin Oncol , vol.18 , pp. 1606-1613
    • Peters III, W.A.1    Liu, P.Y.2    Barrett, I.I.R.J.3
  • 34
    • 33746512512 scopus 로고    scopus 로고
    • Principal components analysis corrects for stratification in genome-wide association studies
    • Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, and Reich D. (2006). Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38, 904-909
    • (2006) Nat Genet , vol.38 , pp. 904-909
    • Price, A.L.1    Patterson, N.J.2    Plenge, R.M.3    Weinblatt, M.E.4    Shadick, N.A.5    Reich, D.6
  • 35
    • 33748324572 scopus 로고    scopus 로고
    • Single nucleotide polymorphisms in DNA repair genes might be prognostic factors in muscle-invasive bladder cancer patients treated with chemoradiotherapy
    • Sakano S, Wada T, Matsumoto H, et al. (2006). Single nucleotide polymorphisms in DNA repair genes might be prognostic factors in muscle-invasive bladder cancer patients treated with chemoradiotherapy. Br J Cancer 95, 561-570
    • (2006) Br J Cancer , vol.95 , pp. 561-570
    • Sakano, S.1    Wada, T.2    Matsumoto, H.3
  • 36
    • 43249110205 scopus 로고    scopus 로고
    • In vivo response to methotrexate forecasts outcome of acute lymphoblastic leukemia and has a distinct gene expression profile
    • Sorich MJ, Pottier N, Pei D, et al. (2008). In vivo response to methotrexate forecasts outcome of acute lymphoblastic leukemia and has a distinct gene expression profile. PLoSMed 5, e83
    • (2008) PLoSMed , vol.5
    • Sorich, M.J.1    Pottier, N.2    Pei, D.3
  • 37
    • 0036020892 scopus 로고    scopus 로고
    • A direct approach to false discovery rates
    • Storey JD. (2002). A direct approach to false discovery rates. J Royal Statist Soc Series B 64, 479-498
    • (2002) J Royal Statist Soc Series B , vol.64 , pp. 479-498
    • Storey, J.D.1
  • 38
    • 73649104101 scopus 로고    scopus 로고
    • Circulating lamin b1 (lmnb1) biomarker detects early stages of liver cancer in patients
    • Sun S, Xu MZ, Poon RT, Day PJ, and Luk JM (2010). Circulating Lamin B1 (LMNB1) biomarker detects early stages of liver cancer in patients. J Proteome Res 9, 70-78
    • (2010) J Proteome Res , vol.9 , pp. 70-78
    • Sun, S.1    Xu, M.Z.2    Poon, R.T.3    Day, P.J.4    Luk, J.M.5
  • 39
    • 80052442469 scopus 로고    scopus 로고
    • Genetic variation predicting cisplatin cytotoxicity associated with overall survival in lung cancer patients receiving platinum-based chemotherapy
    • Tan XL, Moyer AM, Fridley BL, et al. (2011). Genetic variation predicting cisplatin cytotoxicity associated with overall survival in lung cancer patients receiving platinum-based chemotherapy. Clin Cancer Res 17, 5801-5811
    • (2011) Clin Cancer Res , vol.17 , pp. 5801-5811
    • Tan, X.L.1    Moyer, A.M.2    Fridley, B.L.3
  • 40
    • 25444472585 scopus 로고    scopus 로고
    • Pathway level analysis of gene expression using singular value decomposition
    • Tomfohr J, Lu J, and Kepler TB. (2005). Pathway level analysis of gene expression using singular value decomposition. BMC Bioinformatics 6, 225
    • (2005) BMC Bioinformatics , vol.6 , pp. 225
    • Tomfohr, J.1    Lu, J.2    Kepler, T.B.3
  • 42
    • 0042425741 scopus 로고    scopus 로고
    • Characterization of gene expression profiles associated with glioma progression using oligonucleotide-based microarray analysis and real-Time reverse transcription-polymerase chain reaction
    • Van Den Boom J, Wolter M, Kuick R, et al. (2003). Characterization of gene expression profiles associated with glioma progression using oligonucleotide-based microarray analysis and real-Time reverse transcription-polymerase chain reaction. Am J Pathol 163, 1033-1043
    • (2003) Am J Pathol , vol.163 , pp. 1033-1043
    • Van Den Boom, J.1    Wolter, M.2    Kuick, R.3
  • 44
    • 79960393247 scopus 로고    scopus 로고
    • Genetic profiling' and ovarian cancer therapy (review
    • Vella N, Aiello M, Russo AE, et al. (2011). 'Genetic profiling' and ovarian cancer therapy (review). Mol Med Report 4, 771-777
    • (2011) Mol Med Report , vol.4 , pp. 771-777
    • Vella, N.1    Aiello, M.2    Russo, A.E.3
  • 45
    • 17644379063 scopus 로고    scopus 로고
    • A note on exact tests of Hardy-Weinberg equilibrium
    • Wigginton JE, Cutler DJ, and Abecasis GR. (2005). A note on exact tests of Hardy-Weinberg equilibrium. Am J Hum Genet 76, 887-893
    • (2005) Am J Hum Genet , vol.76 , pp. 887-893
    • Wigginton, J.E.1    Cutler, D.J.2    Abecasis, G.R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.