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Volumn 35, Issue 16, 2007, Pages

Filtering genes to improve sensitivity in oligonucleotide microarray data analysis

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; CONTROLLED STUDY; DATA ANALYSIS; DNA HYBRIDIZATION; DNA MICROARRAY; DNA PROBE; EXPERIMENTAL STUDY; FILTRATION; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC ALGORITHM; GENETIC DATABASE; INTERMETHOD COMPARISON; MICROARRAY ANALYSIS; MOUSE; NONHUMAN; PRIORITY JOURNAL; RETINA DEGENERATION; SENSITIVITY ANALYSIS; ALGORITHM; ANIMAL; C3H MOUSE; COMPARATIVE STUDY; COMPUTER PROGRAM; EVALUATION; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; METHODOLOGY; OLIGONUCLEOTIDE PROBE; STATISTICAL MODEL;

EID: 34548810242     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm537     Document Type: Article
Times cited : (42)

References (40)
  • 3
    • 33745023798 scopus 로고    scopus 로고
    • A reanalysis of a published affymetrix genechip control dataset
    • Dabney,A. and Storey,J. (2006) A reanalysis of a published affymetrix genechip control dataset. Gen. Biol., 7, 401.
    • (2006) Gen. Biol , vol.7 , pp. 401
    • Dabney, A.1    Storey, J.2
  • 4
    • 5144229762 scopus 로고    scopus 로고
    • Immediate gene expression changes after the first course of neoadjuvant chemotherapy in patients with primary breast cancer disease
    • Modlich,O., Prisack,H.-B., Munnes,M., Audretsch,W. and Bojar,H. (2004) Immediate gene expression changes after the first course of neoadjuvant chemotherapy in patients with primary breast cancer disease. Clin. Cancer Res., 10, 6418-6431.
    • (2004) Clin. Cancer Res , vol.10 , pp. 6418-6431
    • Modlich, O.1    Prisack, H.-B.2    Munnes, M.3    Audretsch, W.4    Bojar, H.5
  • 5
    • 0035970050 scopus 로고    scopus 로고
    • Analysis of gene expression profiles in normal and neoplastic ovarian tissue samples identifies candidate molecular markers of epithelial ovarian cancer
    • Welsh,J.B., Zarrinkar,P.P., Sapinoso,L.M., Kern,S.G., Behling,C.A., Monk,B.J., Lockhart,D.J., Burger,R.A. and Hampton,G.M. (2001) Analysis of gene expression profiles in normal and neoplastic ovarian tissue samples identifies candidate molecular markers of epithelial ovarian cancer. PNAS, 98, 1176-1181.
    • (2001) PNAS , vol.98 , pp. 1176-1181
    • Welsh, J.B.1    Zarrinkar, P.P.2    Sapinoso, L.M.3    Kern, S.G.4    Behling, C.A.5    Monk, B.J.6    Lockhart, D.J.7    Burger, R.A.8    Hampton, G.M.9
  • 8
    • 33750179033 scopus 로고    scopus 로고
    • Bignotti,E., Tassi,R.A., Calza,S., Ravaggi,A., Romani,C., Rossi,E., Falchetti,M., Odicino.F.E., Pecorelli,S. et al. (2006) Differential gene expression profiles between tumor biopsies and short-term primary cultures of ovarian serous carcinomas: Identification of novel molecular biomarkers for early diagnosis and therapy. Gynecol. Oncol., 103, 405-416.
    • Bignotti,E., Tassi,R.A., Calza,S., Ravaggi,A., Romani,C., Rossi,E., Falchetti,M., Odicino.F.E., Pecorelli,S. et al. (2006) Differential gene expression profiles between tumor biopsies and short-term primary cultures of ovarian serous carcinomas: Identification of novel molecular biomarkers for early diagnosis and therapy. Gynecol. Oncol., 103, 405-416.
  • 9
    • 15944367439 scopus 로고    scopus 로고
    • Transcriptional profiling reveals evidence for signaling and oligodendroglial abnormalities in the temporal cortex from patients with major depressive disorder
    • Aston,C., Jiang,L. and Sokolov,B.P. (2005) Transcriptional profiling reveals evidence for signaling and oligodendroglial abnormalities in the temporal cortex from patients with major depressive disorder. Mol. Psychiatry, 10, 309-312.
    • (2005) Mol. Psychiatry , vol.10 , pp. 309-312
    • Aston, C.1    Jiang, L.2    Sokolov, B.P.3
  • 10
    • 34447632167 scopus 로고    scopus 로고
    • Pawitan,Y., Bjohle,J., Amler,L., Borg,A.-L., Egyhazi,S., Hall.P., Han,X., Holmberg,L., Huang,F. et al. (2005) Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts. Breast Cancer Res., 7, R953-R964.
    • Pawitan,Y., Bjohle,J., Amler,L., Borg,A.-L., Egyhazi,S., Hall.P., Han,X., Holmberg,L., Huang,F. et al. (2005) Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts. Breast Cancer Res., 7, R953-R964.
  • 11
    • 34548762019 scopus 로고    scopus 로고
    • Affymetrix Statistical Algorithms Description Document (2002).
    • Affymetrix Statistical Algorithms Description Document (2002).
  • 12
    • 12344280017 scopus 로고    scopus 로고
    • Irizarry,R.A., Bolstad,B.M., Collin,F., Cope,L.M., Hobbs,B. and Speed.T.P. (2003) Summaries of Affymetrix GeneChip probe level data. Nucl. Acids Res., 31, e15.
    • Irizarry,R.A., Bolstad,B.M., Collin,F., Cope,L.M., Hobbs,B. and Speed.T.P. (2003) Summaries of Affymetrix GeneChip probe level data. Nucl. Acids Res., 31, e15.
  • 13
    • 33645143721 scopus 로고    scopus 로고
    • Effects of filtering by present call on analysis of microarray experiments
    • McClintick,J. and Edenberg,H. (2006) Effects of filtering by present call on analysis of microarray experiments. BMC Bioinform., 7 49.
    • (2006) BMC Bioinform , vol.7 , pp. 49
    • McClintick, J.1    Edenberg, H.2
  • 14
    • 22144461265 scopus 로고    scopus 로고
    • Preferred analysis methods for affymetrix genechips revealed by a wholly defined control dataset
    • Choe,S., Boutros,M., Michelson,A., Church,G. and Halfon,M. (2005) Preferred analysis methods for affymetrix genechips revealed by a wholly defined control dataset. Gen. Biol., 6, R16.
    • (2005) Gen. Biol , vol.6
    • Choe, S.1    Boutros, M.2    Michelson, A.3    Church, G.4    Halfon, M.5
  • 15
    • 0026659476 scopus 로고
    • Photoreceptor-specific mrnas in mice carrying different allelic combinations at the rd and rds loci
    • Viczian,A., Sanyal,S., Toffenetti,J., Chader,G. and Farber,D. (1992) Photoreceptor-specific mrnas in mice carrying different allelic combinations at the rd and rds loci. Exp. Eye Res., 54, 853-860.
    • (1992) Exp. Eye Res , vol.54 , pp. 853-860
    • Viczian, A.1    Sanyal, S.2    Toffenetti, J.3    Chader, G.4    Farber, D.5
  • 17
    • 0016207067 scopus 로고
    • Ribonucleic acid isolated by cesium chloride centrifugation
    • Glisin,V., Crkvenjakov,R. and Byus,C. (1974) Ribonucleic acid isolated by cesium chloride centrifugation. Biochemistry, 13, 2633-2637.
    • (1974) Biochemistry , vol.13 , pp. 2633-2637
    • Glisin, V.1    Crkvenjakov, R.2    Byus, C.3
  • 18
    • 33644858587 scopus 로고    scopus 로고
    • Multidimensional local false discovery rate for microarray studies
    • Ploner,A., Calza,S., Gusnanto,A. and Pawitan,Y. (2006) Multidimensional local false discovery rate for microarray studies. Bioinformatics, 22, 556-565.
    • (2006) Bioinformatics , vol.22 , pp. 556-565
    • Ploner, A.1    Calza, S.2    Gusnanto, A.3    Pawitan, Y.4
  • 19
    • 34548773483 scopus 로고    scopus 로고
    • Bolstad,B, 2006 affyPLM: Methods for fitting probe-level models R package version 1.8.0
    • Bolstad,B. (2006) affyPLM: Methods for fitting probe-level models R package version 1.8.0.
  • 20
    • 34548710830 scopus 로고    scopus 로고
    • Feature level exploration of the choe et al affymetrix genechip control dataset
    • Technical Report Working Paper 102 Johns Hopkins University, Department of Biostatistics Working Papers
    • Irizarry,R.A., Cope,L., and Wu,Z. (2006) Feature level exploration of the choe et al affymetrix genechip control dataset. Technical Report Working Paper 102 Johns Hopkins University, Department of Biostatistics Working Papers.
    • (2006)
    • Irizarry, R.A.1    Cope, L.2    Wu, Z.3
  • 21
    • 0035174883 scopus 로고    scopus 로고
    • Identification by array screening of altered nm23-m2/puf mrna expression in mouse retinal degeneration
    • Jones,S., Jomary,C., Grist,J., Stewart,H. and. Neal,M. (2000). Identification by array screening of altered nm23-m2/puf mrna expression in mouse retinal degeneration. Mol. Cell Biol. Res. Commun., 4 20-25.
    • (2000) Mol. Cell Biol. Res. Commun , vol.4 , pp. 20-25
    • Jones, S.1    Jomary, C.2    Grist, J.3    Stewart, H.4    Neal, M.5
  • 22
    • 4744338189 scopus 로고    scopus 로고
    • Multidestructive pathways triggered in photoreceptor cell death of the rd mouse as determined through gene expression profiling
    • Rohrer,B., Pinto,F., Hulse,K., Lohr,H., Zhang,L. and Almeida,J. (2004) Multidestructive pathways triggered in photoreceptor cell death of the rd mouse as determined through gene expression profiling. J. Biol. Chem., 279, 41903-41910.
    • (2004) J. Biol. Chem , vol.279 , pp. 41903-41910
    • Rohrer, B.1    Pinto, F.2    Hulse, K.3    Lohr, H.4    Zhang, L.5    Almeida, J.6
  • 24
    • 33645356186 scopus 로고    scopus 로고
    • Up-regulation and increased phosphorylation of protein kinase c (pkc) delta, mu and theta in the degenerating rdl mouse retina
    • Azadi,S., Paquet-Durand,F., Medstrand,P., van Veen,T. and Ekstrom,P. (2006) Up-regulation and increased phosphorylation of protein kinase c (pkc) delta, mu and theta in the degenerating rdl mouse retina. Mol. Cell. Neurosci., 31, 759-773.
    • (2006) Mol. Cell. Neurosci , vol.31 , pp. 759-773
    • Azadi, S.1    Paquet-Durand, F.2    Medstrand, P.3    van Veen, T.4    Ekstrom, P.5
  • 26
    • 27444437192 scopus 로고    scopus 로고
    • Mouse mutants as models for congenital retinal disorders
    • Dalke,C. and Graw,J. (2005) Mouse mutants as models for congenital retinal disorders. Exp. Eye Res., 81, 503-512.
    • (2005) Exp. Eye Res , vol.81 , pp. 503-512
    • Dalke, C.1    Graw, J.2
  • 27
    • 0024990758 scopus 로고
    • Retinal degeneration in the rd mouse is caused by a defect in the beta subunit of rod cgmp-phosphodiesterase
    • Bowes,C., Li,T., Danciger,M., Baxter,L., Applebury,M. and Farber,D. (1990) Retinal degeneration in the rd mouse is caused by a defect in the beta subunit of rod cgmp-phosphodiesterase. Nature, 347, 677-678.
    • (1990) Nature , vol.347 , pp. 677-678
    • Bowes, C.1    Li, T.2    Danciger, M.3    Baxter, L.4    Applebury, M.5    Farber, D.6
  • 28
    • 0030781996 scopus 로고    scopus 로고
    • Crx, a novel otx-like paired-homeodomain protein, binds to and transactivates photoreceptor cell-specific genes
    • Chen,S., Wang,Q., Nie,Z., Sun,H., Lennon,G., Copeland,N., Gilbert,D., Jenkins,N. and Zack,D. (1997) Crx, a novel otx-like paired-homeodomain protein, binds to and transactivates photoreceptor cell-specific genes. Neuron, 19, 1017-1030.
    • (1997) Neuron , vol.19 , pp. 1017-1030
    • Chen, S.1    Wang, Q.2    Nie, Z.3    Sun, H.4    Lennon, G.5    Copeland, N.6    Gilbert, D.7    Jenkins, N.8    Zack, D.9
  • 29
    • 0030725687 scopus 로고    scopus 로고
    • Crx, a novel otx-like homeobox gene, shows photoreceptor-specific expression and regulates photoreceptor differentiation
    • Furukawa,T., Morrow,E. and Cepko,C. (1997) Crx, a novel otx-like homeobox gene, shows photoreceptor-specific expression and regulates photoreceptor differentiation. Cell, 91, 531-541.
    • (1997) Cell , vol.91 , pp. 531-541
    • Furukawa, T.1    Morrow, E.2    Cepko, C.3
  • 30
    • 34548772980 scopus 로고    scopus 로고
    • Wu,J. and with contributions from MacDonald,J, Jeff Gentry,R.I, 2006 gcrma: Background Adjustment Using Sequence Information (2006) R package version 2.6.0
    • Wu,J. and with contributions from MacDonald,J., Jeff Gentry,R.I. (2006) gcrma: Background Adjustment Using Sequence Information (2006) R package version 2.6.0.
  • 32
    • 27144545378 scopus 로고    scopus 로고
    • On the optimum number of hypotheses when the number of observations is limited
    • Futschik,A. and Posch,M. (2005) On the optimum number of hypotheses when the number of observations is limited. Stat Sinica, 15, 841-855.
    • (2005) Stat Sinica , vol.15 , pp. 841-855
    • Futschik, A.1    Posch, M.2
  • 33
    • 25444494145 scopus 로고    scopus 로고
    • Correlation test to assess low-level processing of high-density oligonucleotide microarray data
    • Ploner,A., Miller,L.D., Hall,P., Bergh,J. and Pawitan,Y. (2005) Correlation test to assess low-level processing of high-density oligonucleotide microarray data. BMC Bioinform, 6, 80.
    • (2005) BMC Bioinform , vol.6 , pp. 80
    • Ploner, A.1    Miller, L.D.2    Hall, P.3    Bergh, J.4    Pawitan, Y.5
  • 36
    • 27544460141 scopus 로고    scopus 로고
    • Modulation of extracellular matrix genes reflects the magnitude of physiological adaptation to aerobic exercise training in humans
    • Timmons,J.A., Jansson,E., Fischer,H., Gustafsson,T., Greenhaff,P.L., Ridden,J., Rachman,J. and Sundberg,C.J. (2005) Modulation of extracellular matrix genes reflects the magnitude of physiological adaptation to aerobic exercise training in humans. BMC Biol., 3 19.
    • (2005) BMC Biol , vol.3 , pp. 19
    • Timmons, J.A.1    Jansson, E.2    Fischer, H.3    Gustafsson, T.4    Greenhaff, P.L.5    Ridden, J.6    Rachman, J.7    Sundberg, C.J.8
  • 37
  • 38
    • 33646127805 scopus 로고    scopus 로고
    • Gene array expression profiling in acne lesions reveals marked upregulation of genes involved in inflammation and matrix remodeling
    • Trivedi,N.R., Gilliland,K.L., Zhao,W., Liu,W. and Thiboutot,D.M. (2006) Gene array expression profiling in acne lesions reveals marked upregulation of genes involved in inflammation and matrix remodeling. J. Invest. Dermatol., 126, 1071-1079.
    • (2006) J. Invest. Dermatol , vol.126 , pp. 1071-1079
    • Trivedi, N.R.1    Gilliland, K.L.2    Zhao, W.3    Liu, W.4    Thiboutot, D.M.5
  • 39
    • 34548743539 scopus 로고    scopus 로고
    • R Development Core Team. (2006) R: A Language and Environment for Statistical Computing R Foundation for Statistical Computing Vienna, Austria (2006) {ISBN} 3-900051-07-0.
    • R Development Core Team. (2006) R: A Language and Environment for Statistical Computing R Foundation for Statistical Computing Vienna, Austria (2006) {ISBN} 3-900051-07-0.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.