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Volumn 12, Issue SUPPL. 10, 2011, Pages

High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATIC QUALITY CONTROL; BIOMEDICAL RESEARCH; EXPRESSION LEVELS; MICROARRAY DATA SETS; MICROARRAY EXPERIMENTS; PARAMETRIC DISTRIBUTIONS; PUBLICLY ACCESSIBLE; REPRODUCIBILITIES;

EID: 80054094132     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-S10-S2     Document Type: Article
Times cited : (11)

References (31)
  • 6
    • 34247388455 scopus 로고    scopus 로고
    • Meta-analysis of several gene lists for distinct types of cancer: a simple way to reveal common prognostic markers
    • 10.1186/1471-2105-8-118, 1853113, 17411443
    • Yang X, Sun X. Meta-analysis of several gene lists for distinct types of cancer: a simple way to reveal common prognostic markers. BMC Bioinformatics 2007, 8:118. 10.1186/1471-2105-8-118, 1853113, 17411443.
    • (2007) BMC Bioinformatics , vol.8 , pp. 118
    • Yang, X.1    Sun, X.2
  • 7
    • 0036682376 scopus 로고    scopus 로고
    • Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer
    • Rhodes DR, Barrette TR, Rubin MA, Ghosh D, Chinnaiyan AM. Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Res 2002, 62(15):4427-4433.
    • (2002) Cancer Res , vol.62 , Issue.15 , pp. 4427-4433
    • Rhodes, D.R.1    Barrette, T.R.2    Rubin, M.A.3    Ghosh, D.4    Chinnaiyan, A.M.5
  • 8
    • 67649205713 scopus 로고    scopus 로고
    • A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide
    • 10.1093/bioinformatics/btp290, 2732319, 19447786
    • Wren JD. A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide. Bioinformatics 2009, 25(13):1694-1701. 10.1093/bioinformatics/btp290, 2732319, 19447786.
    • (2009) Bioinformatics , vol.25 , Issue.13 , pp. 1694-1701
    • Wren, J.D.1
  • 9
    • 3042514191 scopus 로고    scopus 로고
    • Coexpression analysis of human genes across many microarray data sets
    • 10.1101/gr.1910904, 419787, 15173114
    • Lee HK, Hsu AK, Sajdak J, Qin J, Pavlidis P. Coexpression analysis of human genes across many microarray data sets. Genome Res 2004, 14(6):1085-1094. 10.1101/gr.1910904, 419787, 15173114.
    • (2004) Genome Res , vol.14 , Issue.6 , pp. 1085-1094
    • Lee, H.K.1    Hsu, A.K.2    Sajdak, J.3    Qin, J.4    Pavlidis, P.5
  • 10
    • 77954697233 scopus 로고    scopus 로고
    • Genome-wide functional annotation by integrating multiple microarray datasets using meta-analysis
    • 10.1504/IJDMB.2010.034194, 20815137
    • Srivastava GP, Qiu J, Xu D. Genome-wide functional annotation by integrating multiple microarray datasets using meta-analysis. Int J Data Min Bioinform 2010, 4(4):357-376. 10.1504/IJDMB.2010.034194, 20815137.
    • (2010) Int J Data Min Bioinform , vol.4 , Issue.4 , pp. 357-376
    • Srivastava, G.P.1    Qiu, J.2    Xu, D.3
  • 12
    • 33646369893 scopus 로고    scopus 로고
    • Strategies for comparing gene expression profiles from different microarray platforms: application to a case-control experiment
    • 10.1016/j.ab.2006.03.023, 16624241
    • Severgnini M, Bicciato S, Mangano E, Scarlatti F, Mezzelani A, Mattioli M, Ghidoni R, Peano C, Bonnal R, Viti F, et al. Strategies for comparing gene expression profiles from different microarray platforms: application to a case-control experiment. Anal Biochem 2006, 353(1):43-56. 10.1016/j.ab.2006.03.023, 16624241.
    • (2006) Anal Biochem , vol.353 , Issue.1 , pp. 43-56
    • Severgnini, M.1    Bicciato, S.2    Mangano, E.3    Scarlatti, F.4    Mezzelani, A.5    Mattioli, M.6    Ghidoni, R.7    Peano, C.8    Bonnal, R.9    Viti, F.10
  • 14
    • 18244378238 scopus 로고    scopus 로고
    • Independence and reproducibility across microarray platforms
    • 10.1038/nmeth757, 15846360
    • Larkin JE, Frank BC, Gavras H, Sultana R, Quackenbush J. Independence and reproducibility across microarray platforms. Nat Methods 2005, 2(5):337-344. 10.1038/nmeth757, 15846360.
    • (2005) Nat Methods , vol.2 , Issue.5 , pp. 337-344
    • Larkin, J.E.1    Frank, B.C.2    Gavras, H.3    Sultana, R.4    Quackenbush, J.5
  • 16
    • 78650735473 scopus 로고    scopus 로고
    • The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models
    • 10.1038/nbt.1665, 20676074
    • Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol 2010, 28(8):827-838. 10.1038/nbt.1665, 20676074.
    • (2010) Nat Biotechnol , vol.28 , Issue.8 , pp. 827-838
    • Shi, L.1    Campbell, G.2    Jones, W.D.3    Campagne, F.4    Wen, Z.5    Walker, S.J.6    Su, Z.7    Chu, T.M.8    Goodsaid, F.M.9    Pusztai, L.10
  • 17
    • 26444563353 scopus 로고    scopus 로고
    • List of lists-annotated (LOLA): a database for annotation and comparison of published microarray gene lists
    • 10.1016/j.gene.2005.07.008, 16140476
    • Cahan P, Ahmad AM, Burke H, Fu S, Lai Y, Florea L, Dharker N, Kobrinski T, Kale P, McCaffrey TA. List of lists-annotated (LOLA): a database for annotation and comparison of published microarray gene lists. Gene 2005, 360(1):78-82. 10.1016/j.gene.2005.07.008, 16140476.
    • (2005) Gene , vol.360 , Issue.1 , pp. 78-82
    • Cahan, P.1    Ahmad, A.M.2    Burke, H.3    Fu, S.4    Lai, Y.5    Florea, L.6    Dharker, N.7    Kobrinski, T.8    Kale, P.9    McCaffrey, T.A.10
  • 18
    • 33744975264 scopus 로고    scopus 로고
    • L2L: a simple tool for discovering the hidden significance in microarray expression data
    • 10.1186/gb-2005-6-9-r81, 1242216, 16168088
    • Newman JC, Weiner AM. L2L: a simple tool for discovering the hidden significance in microarray expression data. Genome Biol 2005, 6(9):R81. 10.1186/gb-2005-6-9-r81, 1242216, 16168088.
    • (2005) Genome Biol , vol.6 , Issue.9
    • Newman, J.C.1    Weiner, A.M.2
  • 20
    • 36448955001 scopus 로고    scopus 로고
    • CellMontage: similar expression profile search server
    • 10.1093/bioinformatics/btm462, 17895274
    • Fujibuchi W, Kiseleva L, Taniguchi T, Harada H, Horton P. CellMontage: similar expression profile search server. Bioinformatics 2007, 23(22):3103-3104. 10.1093/bioinformatics/btm462, 17895274.
    • (2007) Bioinformatics , vol.23 , Issue.22 , pp. 3103-3104
    • Fujibuchi, W.1    Kiseleva, L.2    Taniguchi, T.3    Harada, H.4    Horton, P.5
  • 21
    • 77955287981 scopus 로고    scopus 로고
    • Microarray meta-analysis database (M(2)DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database
    • 10.1186/1471-2105-11-421, 2928207, 20698961
    • Cheng WC, Tsai ML, Chang CW, Huang CL, Chen CR, Shu WY, Lee YS, Wang TH, Hong JH, Li CY, et al. Microarray meta-analysis database (M(2)DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database. BMC Bioinformatics 2010, 11:421. 10.1186/1471-2105-11-421, 2928207, 20698961.
    • (2010) BMC Bioinformatics , vol.11 , pp. 421
    • Cheng, W.C.1    Tsai, M.L.2    Chang, C.W.3    Huang, C.L.4    Chen, C.R.5    Shu, W.Y.6    Lee, Y.S.7    Wang, T.H.8    Hong, J.H.9    Li, C.Y.10
  • 22
    • 34548499539 scopus 로고    scopus 로고
    • Meta-analysis of microarray results: challenges, opportunities, and recommendations for standardization
    • 10.1016/j.gene.2007.06.016, 2111172, 17651921
    • Cahan P, Rovegno F, Mooney D, Newman JC, St Laurent G, McCaffrey TA. Meta-analysis of microarray results: challenges, opportunities, and recommendations for standardization. Gene 2007, 401(1-2):12-18. 10.1016/j.gene.2007.06.016, 2111172, 17651921.
    • (2007) Gene , vol.401 , Issue.1-2 , pp. 12-18
    • Cahan, P.1    Rovegno, F.2    Mooney, D.3    Newman, J.C.4    St Laurent, G.5    McCaffrey, T.A.6
  • 23
    • 38849106351 scopus 로고    scopus 로고
    • A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments
    • 10.1093/bioinformatics/btm620, 18204063
    • Hong F, Breitling R. A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments. Bioinformatics 2008, 24(3):374-382. 10.1093/bioinformatics/btm620, 18204063.
    • (2008) Bioinformatics , vol.24 , Issue.3 , pp. 374-382
    • Hong, F.1    Breitling, R.2
  • 24
    • 77955104946 scopus 로고    scopus 로고
    • Comparison study of microarray meta-analysis methods
    • 10.1186/1471-2105-11-408, 2922198, 20678237
    • Campain A, Yang YH. Comparison study of microarray meta-analysis methods. BMC Bioinformatics 2010, 11:408. 10.1186/1471-2105-11-408, 2922198, 20678237.
    • (2010) BMC Bioinformatics , vol.11 , pp. 408
    • Campain, A.1    Yang, Y.H.2
  • 25
    • 1542309545 scopus 로고    scopus 로고
    • Statistical issues and methods for meta-analysis of microarray data: a case study in prostate cancer
    • 10.1007/s10142-003-0087-5, 12884057
    • Ghosh D, Barette TR, Rhodes D, Chinnaiyan AM. Statistical issues and methods for meta-analysis of microarray data: a case study in prostate cancer. Funct Integr Genomics 2003, 3(4):180-188. 10.1007/s10142-003-0087-5, 12884057.
    • (2003) Funct Integr Genomics , vol.3 , Issue.4 , pp. 180-188
    • Ghosh, D.1    Barette, T.R.2    Rhodes, D.3    Chinnaiyan, A.M.4
  • 27
    • 71049170436 scopus 로고    scopus 로고
    • Internal standard-based analysis of microarray data. Part 1: analysis of differential gene expressions
    • 10.1093/nar/gkp706, 2770671, 19720734
    • Dozmorov I, Lefkovits I. Internal standard-based analysis of microarray data. Part 1: analysis of differential gene expressions. Nucleic Acids Res 2009, 37(19):6323-6339. 10.1093/nar/gkp706, 2770671, 19720734.
    • (2009) Nucleic Acids Res , vol.37 , Issue.19 , pp. 6323-6339
    • Dozmorov, I.1    Lefkovits, I.2
  • 28
    • 2942542735 scopus 로고    scopus 로고
    • Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment
    • 10.1186/1471-2105-5-5, 333424, 14718068
    • Konishi T. Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment. BMC Bioinformatics 2004, 5:5. 10.1186/1471-2105-5-5, 333424, 14718068.
    • (2004) BMC Bioinformatics , vol.5 , pp. 5
    • Konishi, T.1
  • 29
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • 10.1093/bioinformatics/19.2.185, 12538238
    • Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19(2):185-193. 10.1093/bioinformatics/19.2.185, 12538238.
    • (2003) Bioinformatics , vol.19 , Issue.2 , pp. 185-193
    • Bolstad, B.M.1    Irizarry, R.A.2    Astrand, M.3    Speed, T.P.4
  • 31
    • 80054091152 scopus 로고    scopus 로고
    • Global meta-analysis of 1-color microarray experiments accurately predicts gene ontology categories
    • 3044268, 21342543
    • Dozmorov MG, Giles CB, Wren JD. Global meta-analysis of 1-color microarray experiments accurately predicts gene ontology categories. BMC Bioinformatics 2011, 12(Suppl 10):S14. 3044268, 21342543.
    • (2011) BMC Bioinformatics , vol.12 , Issue.SUPPL. 10
    • Dozmorov, M.G.1    Giles, C.B.2    Wren, J.D.3


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