메뉴 건너뛰기




Volumn 103, Issue 1, 2014, Pages 21-30

Avoiding pitfalls in gene (co)expression meta-analysis

Author keywords

Cancer gene expression; Differential coexpression; Differential expression; Microarray data processing

Indexed keywords

ARTICLE; BREAST CANCER; COLON CANCER; DATA PROCESSING; GENE COEXPRESSION; GENE EXPRESSION; LUNG CANCER; MICROARRAY ANALYSIS; PRIORITY JOURNAL; SAMPLE SIZE; TUMOR GENE;

EID: 84895890663     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2013.10.006     Document Type: Article
Times cited : (9)

References (33)
  • 2
    • 27144486151 scopus 로고    scopus 로고
    • Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms
    • Barnes M., Freudenberg J., Thompson S., Aronow B., Pavlidis P. Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms. Nucleic Acids Res. 2005, 33(18):5914-5923.
    • (2005) Nucleic Acids Res. , vol.33 , Issue.18 , pp. 5914-5923
    • Barnes, M.1    Freudenberg, J.2    Thompson, S.3    Aronow, B.4    Pavlidis, P.5
  • 4
    • 22144461265 scopus 로고    scopus 로고
    • Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset
    • Choe S.E., Boutros M., Michelson A.M., Church G.M., Halfon M.S. Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol. 2005, 6:R16.
    • (2005) Genome Biol. , vol.6
    • Choe, S.E.1    Boutros, M.2    Michelson, A.M.3    Church, G.M.4    Halfon, M.S.5
  • 5
    • 34547871639 scopus 로고    scopus 로고
    • GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor
    • Davis S., Meltzer P.S. GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. Bioinformatics 2007, 23:1846-1847.
    • (2007) Bioinformatics , vol.23 , pp. 1846-1847
    • Davis, S.1    Meltzer, P.S.2
  • 6
    • 77953913791 scopus 로고    scopus 로고
    • From 'differential expression' to 'differential networking' - identification of dysfunctional regulatory networks in diseases
    • de la Fuente A. From 'differential expression' to 'differential networking' - identification of dysfunctional regulatory networks in diseases. Trends Genet. 2010, 26:326-333.
    • (2010) Trends Genet. , vol.26 , pp. 326-333
    • de la Fuente, A.1
  • 8
    • 1342288026 scopus 로고    scopus 로고
    • Affy - Analysis of Affymetrix GeneChip data at the probe level
    • Gautier L., Cope L., Bolstad B.M., Irizarry R.A. affy - Analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 2004, 20:307-315.
    • (2004) Bioinformatics , vol.20 , pp. 307-315
    • Gautier, L.1    Cope, L.2    Bolstad, B.M.3    Irizarry, R.A.4
  • 11
    • 55949116984 scopus 로고    scopus 로고
    • A snapshot of microarray-generated gene expression signatures associated with ovarian carcinoma
    • Gyorffy B., Dietel M., Fekete T., Lage H. A snapshot of microarray-generated gene expression signatures associated with ovarian carcinoma. Int J. Gynecol. Cancer 2008, 18:1215-1233.
    • (2008) Int J. Gynecol. Cancer , vol.18 , pp. 1215-1233
    • Gyorffy, B.1    Dietel, M.2    Fekete, T.3    Lage, H.4
  • 12
    • 77958449045 scopus 로고    scopus 로고
    • Stable feature selection for biomarker discovery
    • He Z., Yu W. Stable feature selection for biomarker discovery. Comput Biol. Chem. 2010, 34:215-225.
    • (2010) Comput Biol. Chem. , vol.34 , pp. 215-225
    • He, Z.1    Yu, W.2
  • 13
    • 56549116918 scopus 로고    scopus 로고
    • Implementing a class of permutation tests: the coin package
    • Hothorn T., Hornik K., Wiel M.A.v.d, Zeileis A. Implementing a class of permutation tests: the coin package. J. Stat. Softw. 2008, 28:1-23.
    • (2008) J. Stat. Softw. , vol.28 , pp. 1-23
    • Hothorn, T.1    Hornik, K.2    Wiel, M.D.3    Zeileis, A.4
  • 14
    • 3142767437 scopus 로고    scopus 로고
    • Estrogen receptor-alpha polymorphism in a Taiwanese clinical breast cancer population: a case-control study
    • Hsiao W.C., Young K.C., Lin S.L., Lin P.W. Estrogen receptor-alpha polymorphism in a Taiwanese clinical breast cancer population: a case-control study. Breast Cancer Res. 2004, 6:R180-R186.
    • (2004) Breast Cancer Res. , vol.6
    • Hsiao, W.C.1    Young, K.C.2    Lin, S.L.3    Lin, P.W.4
  • 15
    • 67049159812 scopus 로고    scopus 로고
    • A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation
    • Hudson N.J., Reverter A., Dalrymple B.P. A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation. PLoS Comput. Biol. 2009, 5:e1000382.
    • (2009) PLoS Comput. Biol. , vol.5
    • Hudson, N.J.1    Reverter, A.2    Dalrymple, B.P.3
  • 16
    • 13244268329 scopus 로고    scopus 로고
    • Combining gene expression data from different generations of oligonucleotide arrays
    • Hwang K.B., Kong S.W., Greenberg S.A., Park P.J. Combining gene expression data from different generations of oligonucleotide arrays. BMC Bioinformatics 2004, 5:159.
    • (2004) BMC Bioinformatics , vol.5 , pp. 159
    • Hwang, K.B.1    Kong, S.W.2    Greenberg, S.A.3    Park, P.J.4
  • 17
    • 33645326509 scopus 로고    scopus 로고
    • Comparison of Affymetrix GeneChip expression measures
    • Irizarry R.A., Wu Z., Jaffee H.A. Comparison of Affymetrix GeneChip expression measures. Bioinformatics 2006, 22:789-794.
    • (2006) Bioinformatics , vol.22 , pp. 789-794
    • Irizarry, R.A.1    Wu, Z.2    Jaffee, H.A.3
  • 19
    • 13444249852 scopus 로고    scopus 로고
    • Prediction of cancer outcome with microarrays: a multiple random validation strategy
    • Michiels S., Koscielny S., Hill C. Prediction of cancer outcome with microarrays: a multiple random validation strategy. Lancet 2005, 365:488-492.
    • (2005) Lancet , vol.365 , pp. 488-492
    • Michiels, S.1    Koscielny, S.2    Hill, C.3
  • 20
    • 2342624566 scopus 로고    scopus 로고
    • Microarray reality checks in the context of a complex disease
    • Miklos G.L., Maleszka R. Microarray reality checks in the context of a complex disease. Nat. Biotechnol. 2004, 22:615-621.
    • (2004) Nat. Biotechnol. , vol.22 , pp. 615-621
    • Miklos, G.L.1    Maleszka, R.2
  • 21
    • 67651121480 scopus 로고    scopus 로고
    • Intrinsic bias in breast cancer gene expression data sets
    • Mosley J.D., Keri R.A. Intrinsic bias in breast cancer gene expression data sets. BMC Cancer 2009, 9:214.
    • (2009) BMC Cancer , vol.9 , pp. 214
    • Mosley, J.D.1    Keri, R.A.2
  • 24
    • 38649143214 scopus 로고    scopus 로고
    • A comparison of Affymetrix gene expression arrays
    • Robinson M.D., Speed T.P. A comparison of Affymetrix gene expression arrays. BMC Bioinformatics 2007, 8(1):449.
    • (2007) BMC Bioinformatics , vol.8 , Issue.1 , pp. 449
    • Robinson, M.D.1    Speed, T.P.2
  • 27
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response
    • Tusher V.G., Tibshirani R., Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. U. S. A. 2001, 98:5116-5121.
    • (2001) Proc. Natl. Acad. Sci. U. S. A. , vol.98 , pp. 5116-5121
    • Tusher, V.G.1    Tibshirani, R.2    Chu, G.3
  • 31
    • 77952721219 scopus 로고    scopus 로고
    • Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset
    • Zhu Q., Miecznikowski J.C., Halfon M.S. Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset. BMC Bioinformatics 2010, 11:285.
    • (2010) BMC Bioinformatics , vol.11 , pp. 285
    • Zhu, Q.1    Miecznikowski, J.C.2    Halfon, M.S.3
  • 32
    • 56649093037 scopus 로고    scopus 로고
    • GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus
    • Zhu Y., Davis S., Stephens R., Meltzer P.S., Chen Y. GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus. Bioinformatics 2008, 24:2798-2800.
    • (2008) Bioinformatics , vol.24 , pp. 2798-2800
    • Zhu, Y.1    Davis, S.2    Stephens, R.3    Meltzer, P.S.4    Chen, Y.5
  • 33
    • 69249085408 scopus 로고    scopus 로고
    • Stability and aggregation of ranked gene lists
    • Boulesteix A.L., Slawski M. Stability and aggregation of ranked gene lists. Brief Bioinform. Sep. 2009, 10(5):556-568. 10.1093/bib/bbp034.
    • (2009) Brief Bioinform. , vol.10 , Issue.5 , pp. 556-568
    • Boulesteix, A.L.1    Slawski, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.