메뉴 건너뛰기




Volumn 5, Issue 10, 2010, Pages

Systematical detection of significant genes in microarray data by incorporating gene interaction relationship in biological systems

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; CORRELATION COEFFICIENT; DNA MICROARRAY; FALSE POSITIVE RESULT; FUNCTIONAL GENOMICS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENE INTERACTION; GENE MAPPING; GENE MUTATION; GENETIC ASSOCIATION; GENETIC DATABASE; GENETIC MODEL; GENETIC VARIABILITY; INTERMETHOD COMPARISON; NONLINEAR SYSTEM; NORMAL DISTRIBUTION; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; SIMULATION; STUDENT T TEST; SYSTEMS BIOLOGY; ANALYSIS OF VARIANCE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

EID: 78149454849     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0013721     Document Type: Article
Times cited : (4)

References (52)
  • 1
    • 78149423118 scopus 로고    scopus 로고
    • A new test statistic based on shrunken sample variance for identifying differentially expressed genes in small microarray experiments
    • Hirakawa A, Sato Y, Hamada C, Yoshimura I (2008) A new test statistic based on shrunken sample variance for identifying differentially expressed genes in small microarray experiments. Bioinform Biol Insights 2: 145-156.
    • (2008) Bioinform Biol Insights , vol.2 , pp. 145-156
    • Hirakawa, A.1    Sato, Y.2    Hamada, C.3    Yoshimura, I.4
  • 2
    • 33645643565 scopus 로고    scopus 로고
    • A two-sample Bayesian t-test for microarray data
    • Fox RJ, Dimmic MW (2006) A two-sample Bayesian t-test for microarray data. BMC Bioinformatics 7: 126.
    • (2006) BMC Bioinformatics , vol.7 , pp. 126
    • Fox, R.J.1    Dimmic, M.W.2
  • 3
    • 24644493356 scopus 로고    scopus 로고
    • Learning Petri Net Models of Non-linear Gene Interactions
    • Mayo M (2005) Learning Petri Net Models of Non-linear Gene Interactions. Biosystems 82: 74-82.
    • (2005) Biosystems , vol.82 , pp. 74-82
    • Mayo, M.1
  • 4
    • 0034973569 scopus 로고    scopus 로고
    • Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer
    • Marylyn DR, Lance WH, Nady R, Bailey LR, William DD, et al. (2001) Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. American Society of Human Genetics 69: 138-147.
    • (2001) American Society of Human Genetics , vol.69 , pp. 138-147
    • Marylyn, D.R.1    Lance, W.H.2    Nady, R.3    Bailey, L.R.4    William, D.D.5
  • 5
    • 75649151459 scopus 로고    scopus 로고
    • Reconstructing Nonlinear Dynamic Models of Gene Regulation using Stochastic sampling
    • Johanna M, Daniel R, Gerhard R, Karderali L (2009) Reconstructing Nonlinear Dynamic Models of Gene Regulation using Stochastic sampling. BMC Bioinformatics 10: 448-460.
    • (2009) BMC Bioinformatics , vol.10 , pp. 448-460
    • Johanna, M.1    Daniel, R.2    Gerhard, R.3    Karderali, L.4
  • 6
    • 0030756656 scopus 로고    scopus 로고
    • Nonlinear Systems Identification: Autocorrelation vs Autoskewness
    • Michel S, Curley F (1997) Nonlinear Systems Identification: Autocorrelation vs Autoskewness. Journal of Applied Physiology 83: 975-993.
    • (1997) Journal of Applied Physiology , vol.83 , pp. 975-993
    • Michel, S.1    Curley, F.2
  • 8
    • 12044257427 scopus 로고
    • Kurtosis, Skewness, and Non-Gaussian Cosmological Density Perturbations
    • Luo X, Schramm DN (1993) Kurtosis, Skewness, and Non-Gaussian Cosmological Density Perturbations. The Astrophysical Journal 408: 33-42.
    • (1993) The Astrophysical Journal , vol.408 , pp. 33-42
    • Luo, X.1    Schramm, D.N.2
  • 11
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of Microarray applied to the ionizing radiation response
    • Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of Microarray applied to the ionizing radiation response. Proc Natl Acad Sci USA 98: 5116-5121.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 5116-5121
    • Tusher, V.G.1    Tibshirani, R.2    Chu, G.3
  • 12
    • 0033569406 scopus 로고    scopus 로고
    • Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring
    • Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, et al. (1999) Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science 286: 531-537.
    • (1999) Science , vol.286 , pp. 531-537
    • Golub, T.R.1    Slonim, D.K.2    Tamayo, P.3    Huard, C.4    Gaasenbeek, M.5
  • 13
    • 16244362244 scopus 로고    scopus 로고
    • A gene expression map of Arabidopsis thaliana development
    • Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, et al. (2005) A gene expression map of Arabidopsis thaliana development. Nat Genet 37: 501-506.
    • (2005) Nat Genet , vol.37 , pp. 501-506
    • Schmid, M.1    Davison, T.S.2    Henz, S.R.3    Pape, U.J.4    Demar, M.5
  • 14
    • 33748644662 scopus 로고    scopus 로고
    • Probe-level measurement error improves accuracy in detecting differential gene expression
    • Liu X, Milo M, Lawrence ND, Rattray M (2006) Probe-level measurement error improves accuracy in detecting differential gene expression. Bioinformatics 22: 2107-2113.
    • (2006) Bioinformatics , vol.22 , pp. 2107-2113
    • Liu, X.1    Milo, M.2    Lawrence, N.D.3    Rattray, M.4
  • 15
    • 27644528185 scopus 로고    scopus 로고
    • Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential
    • Shi L, Tong W, Fang H, Scherf U, Han J, et al. (2005) Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential. BMC Bioinformatics 6 Suppl 2: S12.
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 2
    • Shi, L.1    Tong, W.2    Fang, H.3    Scherf, U.4    Han, J.5
  • 17
    • 33750943221 scopus 로고    scopus 로고
    • Ranking Analysis of Microarray Data: A Powerful Method for Identifying Different Expressed Genes
    • Tan YD, MyriamFornage, Fu YX (2006) Ranking Analysis of Microarray Data: A Powerful Method for Identifying Different Expressed Genes. Genomics 88: 846-854.
    • (2006) Genomics , vol.88 , pp. 846-854
    • Tan, Y.D.1    Myriamfornage, F.Y.X.2
  • 18
    • 34147123145 scopus 로고    scopus 로고
    • The Optimal Discovery Procedure for Large-scale Significance Testing, With Application to Comparative Microarray Experiments
    • Storey JD, Dai JY, Leek JT (2007) The Optimal Discovery Procedure for Large-scale Significance Testing, With Application to Comparative Microarray Experiments. Biostatistics 8: 414-432.
    • (2007) Biostatistics , vol.8 , pp. 414-432
    • Storey, J.D.1    Dai, J.Y.2    Leek, J.T.3
  • 19
    • 25144474547 scopus 로고    scopus 로고
    • Hotelling' T2 Multivariate profiling for detecting differential expression in microarrays
    • LuYan, Liu PY, XiaoPeng, Deng HW. (2005) Hotelling' T2 Multivariate profiling for detecting differential expression in microarrays. Bioinformatics 21: 3105-3113.
    • (2005) Bioinformatics , vol.21 , pp. 3105-3113
    • Luyan, L.P.Y.1    Xiao, P.D.H.W.2
  • 20
    • 24144445705 scopus 로고    scopus 로고
    • Improved Statistical Tests for Differential Gene Expression by Shrinking Variance Components
    • Cui XQ, Hwang JTG, Qiu J (2005) Improved Statistical Tests for Differential Gene Expression by Shrinking Variance Components. Biostatistics 6: 59-75.
    • (2005) Biostatistics , vol.6 , pp. 59-75
    • Cui, X.Q.1    Hwang, J.T.G.2    Qiu, J.3
  • 21
    • 0037276175 scopus 로고    scopus 로고
    • Statistical tests for differential expression in cDNA microarray experiments
    • Cui XQ, Churchill GA (2003) Statistical tests for differential expression in cDNA microarray experiments. Genome Biology 4: 210.
    • (2003) Genome Biology , vol.4 , pp. 210
    • Cui, X.Q.1    Churchill, G.A.2
  • 26
    • 0034948896 scopus 로고    scopus 로고
    • A Bayesian framework for the analysis of microarray expression data: Regularized t-test and statistical inferences of gene changes
    • Baldi P, Long AD (2001) A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinfomatics 17: 509-519.
    • (2001) Bioinfomatics , vol.17 , pp. 509-519
    • Baldi, P.1    Long, A.D.2
  • 27
    • 65849488472 scopus 로고    scopus 로고
    • Intra-Platform Repeatability and Inter-Platform Comparability of MicroRNA Microarray Technology
    • Sato F, Tsuchiya S, Terasawa K, Tsujimoto G (2009) Intra-Platform Repeatability and Inter-Platform Comparability of MicroRNA Microarray Technology. PLoS One 4(5): e5540.
    • (2009) PLoS One , vol.4 , Issue.5
    • Sato, F.1    Tsuchiya, S.2    Terasawa, K.3    Tsujimoto, G.4
  • 28
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genomewide studies
    • John DS, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci USA 100: 9440-9445.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 9440-9445
    • John, D.S.1    Tibshirani, R.2
  • 30
    • 22144461265 scopus 로고    scopus 로고
    • Preferred Analysis Methods for Affymetrix GeneChips Revealed by A Wholly Defined Control Dataset
    • Choe SE, Boutros M, Michelson AM, Church GM, Halfon MS (2005) Preferred Analysis Methods for Affymetrix GeneChips Revealed by A Wholly Defined Control Dataset. Genome Biolgoy 6: 16-28.
    • (2005) Genome Biolgoy , vol.6 , pp. 16-28
    • Choe, S.E.1    Boutros, M.2    Michelson, A.M.3    Church, G.M.4    Halfon, M.S.5
  • 31
    • 0037069938 scopus 로고    scopus 로고
    • Down-regulation of caspase 3 in breast cancer: A possible mechanism for chemoresistance
    • Devarajan E, Sahin AA, Chen JS, Krishnamurthy RR, Aggarwal N, et al. (2002) Down-regulation of caspase 3 in breast cancer: a possible mechanism for chemoresistance. Oncogene 21: 8843-8851.
    • (2002) Oncogene , vol.21 , pp. 8843-8851
    • Devarajan, E.1    Sahin, A.A.2    Chen, J.S.3    Krishnamurthy, R.R.4    Aggarwal, N.5
  • 33
    • 0037221767 scopus 로고    scopus 로고
    • TP53 and breast cancer
    • Børresen-Dale AL (2003) TP53 and breast cancer. Hum Mutat 21: 292-300.
    • (2003) Hum Mutat , vol.21 , pp. 292-300
    • Børresen-Dale, A.L.1
  • 34
    • 34250760957 scopus 로고    scopus 로고
    • TP53 mutation status and gene expression profiles are powerful prognostic markers of breast cancer
    • Langerød A, Zhao H, Borgan Ø, Nesland JM, Bukholm IR, et al. (2007) TP53 mutation status and gene expression profiles are powerful prognostic markers of breast cancer. Breast Cancer Research 9: R30.
    • (2007) Breast Cancer Research , vol.9
    • Langerød, A.1    Zhao, H.2    Borgan, O.3    Nesland, J.M.4    Bukholm, I.R.5
  • 36
    • 43149126354 scopus 로고    scopus 로고
    • CCND1 amplification and cyclin D1 expression in breast cancer and their relation with proteomic subgroups and patient outcome
    • Elsheikh S, Green AR, Aleskandarany MA, Grainge M, Paish CE, et al. (2008) CCND1 amplification and cyclin D1 expression in breast cancer and their relation with proteomic subgroups and patient outcome. Breast Cancer Research and Treatment 109: 325-335.
    • (2008) Breast Cancer Research and Treatment , vol.109 , pp. 325-335
    • Elsheikh, S.1    Green, A.R.2    Aleskandarany, M.A.3    Grainge, M.4    Paish, C.E.5
  • 37
    • 28844488762 scopus 로고    scopus 로고
    • Alteration on the expression of IL-1, PDGF, TGF-beta, EGF, and FGF receptors and c-Fos and c-Myc proteins in bone marrow mesenchymal stroma cells from advanced untreated lung and breast cancer patients
    • Hofer EL, La Russa V, Honegger AE, Bullorsky EO, Bordenave RH, et al. (2005) Alteration on the expression of IL-1, PDGF, TGF-beta, EGF, and FGF receptors and c-Fos and c-Myc proteins in bone marrow mesenchymal stroma cells from advanced untreated lung and breast cancer patients. Stem Cells Dev 14: 587-594.
    • (2005) Stem Cells Dev , vol.14 , pp. 587-594
    • Hofer, E.L.1    la Russa, V.2    Honegger, A.E.3    Bullorsky, E.O.4    Bordenave, R.H.5
  • 38
    • 74049105681 scopus 로고    scopus 로고
    • WNT signaling enhances breast cancer cell motility and blockade of the WNT pathway by sFRP1 suppresses MDA-MB-23 xenograft growth
    • Masuda Y, Schlange T, Oakeley EJ, Boulay A, Hynes NE (2009) WNT signaling enhances breast cancer cell motility and blockade of the WNT pathway by sFRP1 suppresses MDA-MB-23 xenograft growth. Breast Cancer Research 11: R32.
    • (2009) Breast Cancer Research , vol.11
    • Masuda, Y.1    Schlange, T.2    Oakeley, E.J.3    Boulay, A.4    Hynes, N.E.5
  • 39
    • 0035719960 scopus 로고    scopus 로고
    • Wnt signaling in breast cancer: Have we come full circle?
    • Brown AM (2001) Wnt signaling in breast cancer: have we come full circle? Breast Cancer Research 3: 351-355.
    • (2001) Breast Cancer Research , vol.3 , pp. 351-355
    • Brown, A.M.1
  • 40
    • 0141995804 scopus 로고    scopus 로고
    • WIF1, a component of the Wnt Pathway, is down-regulated in prostate, breast,lung, and bladder cancer
    • Wissmann C, Wild PJ, Kaiser S, Roepcke S, Stoehr R, et al. (2003) WIF1, a component of the Wnt Pathway, is down-regulated in prostate, breast,lung, and bladder cancer. The Journal of Pathology 201: 204-212.
    • (2003) The Journal of Pathology , vol.201 , pp. 204-212
    • Wissmann, C.1    Wild, P.J.2    Kaiser, S.3    Roepcke, S.4    Stoehr, R.5
  • 41
    • 34548277989 scopus 로고    scopus 로고
    • Genetic Screen for Chromosome Instability in Mice: Mcm4 and breast cancer
    • Shima N, Buske TR, Schimenti JC (2007) Genetic Screen for Chromosome Instability in Mice: Mcm4 and breast cancer. Cell Cycle 6: 1135-1140.
    • (2007) Cell Cycle , vol.6 , pp. 1135-1140
    • Shima, N.1    Buske, T.R.2    Schimenti, J.C.3
  • 42
    • 20444432334 scopus 로고    scopus 로고
    • Toll-Like Receptors on Tumor Cells Facilitate Evasion of Immune Surveillance
    • Huang B, Zhao J, Li H, He KL, Chen Y, et al. (2005) Toll-Like Receptors on Tumor Cells Facilitate Evasion of Immune Surveillance. Cancer Research 65: 5009.
    • (2005) Cancer Research , vol.65 , pp. 5009
    • Huang, B.1    Zhao, J.2    Li, H.3    He, K.L.4    Chen, Y.5
  • 43
    • 37349014037 scopus 로고    scopus 로고
    • Chemopreventive agents induce programmed death-1-ligand 1(PD-L1) surface expression in breast cancer cells and promote PD-L1-mediated T cell apoptosis
    • Zhang P, Su DM, Liang M, Fu J (2008) Chemopreventive agents induce programmed death-1-ligand 1(PD-L1) surface expression in breast cancer cells and promote PD-L1-mediated T cell apoptosis. Molecular Immunology 45: 1470-1476.
    • (2008) Molecular Immunology , vol.45 , pp. 1470-1476
    • Zhang, P.1    Su, D.M.2    Liang, M.3    Fu, J.4
  • 45
    • 0346937461 scopus 로고    scopus 로고
    • Exact Skewness-Kurtosis Tests for Multivariate Normality and Goodness-of-Fit in Multivariate Regression with Application to Asset Pricing Models
    • Dufour JM, Khalaf L, Beaulieu MC (2003) Exact Skewness-Kurtosis Tests for Multivariate Normality and Goodness-of-Fit in Multivariate Regression with Application to Asset Pricing Models. Oxford Bulletin Of Economics And Statistics 65: 891-906.
    • (2003) Oxford Bulletin of Economics and Statistics , vol.65 , pp. 891-906
    • Dufour, J.M.1    Khalaf, L.2    Beaulieu, M.C.3
  • 47
    • 76249130293 scopus 로고    scopus 로고
    • Regulatory interdependence of myeloid transcription factors revealed by matrix RNAi analysis
    • Tomaru Y, Simon C, Forrest AR, Miura H, Kubosaki A, et al. (2009) Regulatory interdependence of myeloid transcription factors revealed by matrix RNAi analysis. Genome Biolgoy 10: R121.
    • (2009) Genome Biolgoy , vol.10
    • Tomaru, Y.1    Simon, C.2    Forrest, A.R.3    Miura, H.4    Kubosaki, A.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.