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Volumn 12, Issue , 2011, Pages

AnyExpress: Integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm

Author keywords

[No Author keywords available]

Indexed keywords

AFFYMETRIX MICROARRAYS; BIOLOGICAL FEATURES; CORRELATION COEFFICIENT; DIFFERENT LAYERS; GENE EXPRESSION DATA; INTEGRATED TOOLKIT; MATCHING ALGORITHM; TIGHTLY-COUPLED;

EID: 79952699174     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-75     Document Type: Article
Times cited : (17)

References (44)
  • 2
    • 53149135477 scopus 로고    scopus 로고
    • Key Issues in Conducting a Meta-Analysis of Gene Expression Microarray Datasets
    • 10.1371/journal.pmed.0050184, 2528050, 18767902
    • Ramasamy A, Mondry A, Holmes CC, Altman DG. Key Issues in Conducting a Meta-Analysis of Gene Expression Microarray Datasets. PLoS Med 2008, 5(9):e184. 10.1371/journal.pmed.0050184, 2528050, 18767902.
    • (2008) PLoS Med , vol.5 , Issue.9
    • Ramasamy, A.1    Mondry, A.2    Holmes, C.C.3    Altman, D.G.4
  • 3
    • 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
  • 4
    • 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
  • 5
    • 27844594381 scopus 로고    scopus 로고
    • Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes
    • 10.1186/1471-2105-6-265, 1312314, 16271137
    • Warnat P, Eils R, Brors B. Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes. BMC Bioinformatics 2005, 6:265. 10.1186/1471-2105-6-265, 1312314, 16271137.
    • (2005) BMC Bioinformatics , vol.6 , pp. 265
    • Warnat, P.1    Eils, R.2    Brors, B.3
  • 7
    • 2442691827 scopus 로고    scopus 로고
    • Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements
    • 10.1093/nar/gnh071, 419626, 15161944
    • Mecham BH, Klus GT, Strovel J, Augustus M, Byrne D, Bozso P, Wetmore DZ, Mariani TJ, Kohane IS, Szallasi Z. Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. Nucleic Acids Res 2004, 32(9):e74. 10.1093/nar/gnh071, 419626, 15161944.
    • (2004) Nucleic Acids Res , vol.32 , Issue.9
    • Mecham, B.H.1    Klus, G.T.2    Strovel, J.3    Augustus, M.4    Byrne, D.5    Bozso, P.6    Wetmore, D.Z.7    Mariani, T.J.8    Kohane, I.S.9    Szallasi, Z.10
  • 8
    • 48349090298 scopus 로고    scopus 로고
    • Effect of polymorphisms within probe-target sequences on olignonucleotide microarray experiments
    • 10.1093/nar/gkn409, 2490733, 18596082
    • Benovoy D, Kwan T, Majewski J. Effect of polymorphisms within probe-target sequences on olignonucleotide microarray experiments. Nucleic Acids Res 2008, 36(13):4417-4423. 10.1093/nar/gkn409, 2490733, 18596082.
    • (2008) Nucleic Acids Res , vol.36 , Issue.13 , pp. 4417-4423
    • Benovoy, D.1    Kwan, T.2    Majewski, J.3
  • 9
    • 33847679625 scopus 로고    scopus 로고
    • Improved precision and accuracy for microarrays using updated probe set definitions
    • 10.1186/1471-2105-8-48, 1805763, 17288599
    • Sandberg R, Larsson O. Improved precision and accuracy for microarrays using updated probe set definitions. BMC Bioinformatics 2007, 8:48. 10.1186/1471-2105-8-48, 1805763, 17288599.
    • (2007) BMC Bioinformatics , vol.8 , pp. 48
    • Sandberg, R.1    Larsson, O.2
  • 10
    • 18744391995 scopus 로고    scopus 로고
    • CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays
    • 10.1093/bioinformatics/bti288, 2819168, 15684227
    • Kong SW, Hwang KB, Kim RD, Zhang BT, Greenberg SA, Kohane IS, Park PJ. CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays. Bioinformatics 2005, 21(9):2116-2117. 10.1093/bioinformatics/bti288, 2819168, 15684227.
    • (2005) Bioinformatics , vol.21 , Issue.9 , pp. 2116-2117
    • Kong, S.W.1    Hwang, K.B.2    Kim, R.D.3    Zhang, B.T.4    Greenberg, S.A.5    Kohane, I.S.6    Park, P.J.7
  • 11
    • 39749096174 scopus 로고    scopus 로고
    • Strategy for encoding and comparison of gene expression signatures
    • 10.1186/gb-2007-8-7-r133, 2323223, 17612401
    • Yi Y, Li C, Miller C, George AL. Strategy for encoding and comparison of gene expression signatures. Genome Biol 2007, 8(7):R133. 10.1186/gb-2007-8-7-r133, 2323223, 17612401.
    • (2007) Genome Biol , vol.8 , Issue.7
    • Yi, Y.1    Li, C.2    Miller, C.3    George, A.L.4
  • 12
    • 70349866711 scopus 로고    scopus 로고
    • Evaluation of a large-scale biomedical data annotation initiative
    • 10.1186/1471-2105-10-S9-S10, 2745681, 19761564
    • Lacson R, Pitzer E, Hinske C, Galante P, Ohno-Machado L. Evaluation of a large-scale biomedical data annotation initiative. BMC Bioinformatics 2009, 10(Suppl 9):S10. 10.1186/1471-2105-10-S9-S10, 2745681, 19761564.
    • (2009) BMC Bioinformatics , vol.10 , Issue.SUPPL. 9
    • Lacson, R.1    Pitzer, E.2    Hinske, C.3    Galante, P.4    Ohno-Machado, L.5
  • 14
    • 70449395274 scopus 로고    scopus 로고
    • Novel software package for cross-platform transcriptome analysis (CPTRA)
    • 10.1186/1471-2105-10-S11-S16, 19811681
    • Zhou X, Su Z, Sammons RD, Peng Y, Tranel PJ, Stewart CN, Yuan JS. Novel software package for cross-platform transcriptome analysis (CPTRA). BMC Bioinformatics 2009, 10(Suppl 11):S16. 10.1186/1471-2105-10-S11-S16, 19811681.
    • (2009) BMC Bioinformatics , vol.10 , Issue.SUPPL. 11
    • Zhou, X.1    Su, Z.2    Sammons, R.D.3    Peng, Y.4    Tranel, P.J.5    Stewart, C.N.6    Yuan, J.S.7
  • 15
    • 33746108159 scopus 로고    scopus 로고
    • A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies
    • 10.1038/nbt1217, 16823376
    • Kuo WP, Liu F, Trimarchi J, Punzo C, Lombardi M, Sarang J, Whipple ME, Maysuria M, Serikawa K, Lee SY, et al. A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat Biotechnol 2006, 24(7):832-840. 10.1038/nbt1217, 16823376.
    • (2006) Nat Biotechnol , vol.24 , Issue.7 , pp. 832-840
    • Kuo, W.P.1    Liu, F.2    Trimarchi, J.3    Punzo, C.4    Lombardi, M.5    Sarang, J.6    Whipple, M.E.7    Maysuria, M.8    Serikawa, K.9    Lee, S.Y.10
  • 16
    • 34347241740 scopus 로고    scopus 로고
    • Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates
    • 10.1186/1471-2164-8-153, 1899500, 17555589
    • Liu F, Jenssen TK, Trimarchi J, Punzo C, Cepko CL, Ohno-Machado L, Hovig E, Kuo WP. Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates. BMC Genomics 2007, 8:153. 10.1186/1471-2164-8-153, 1899500, 17555589.
    • (2007) BMC Genomics , vol.8 , pp. 153
    • Liu, F.1    Jenssen, T.K.2    Trimarchi, J.3    Punzo, C.4    Cepko, C.L.5    Ohno-Machado, L.6    Hovig, E.7    Kuo, W.P.8
  • 21
    • 77951685689 scopus 로고    scopus 로고
    • Incorporating zebrafish omics into chemical biology and toxicology
    • 10.1089/zeb.2009.0636, 20384484
    • Sukardi H, Ung CY, Gong Z, Lam SH. Incorporating zebrafish omics into chemical biology and toxicology. Zebrafish 2010, 7(1):41-52. 10.1089/zeb.2009.0636, 20384484.
    • (2010) Zebrafish , vol.7 , Issue.1 , pp. 41-52
    • Sukardi, H.1    Ung, C.Y.2    Gong, Z.3    Lam, S.H.4
  • 22
    • 57549094171 scopus 로고    scopus 로고
    • Metagenomics approaches in systems microbiology
    • 10.1111/j.1574-6976.2008.00152.x, 19054115
    • Vieites JM, Guazzaroni ME, Beloqui A, Golyshin PN, Ferrer M. Metagenomics approaches in systems microbiology. FEMS Microbiol Rev 2009, 33(1):236-255. 10.1111/j.1574-6976.2008.00152.x, 19054115.
    • (2009) FEMS Microbiol Rev , vol.33 , Issue.1 , pp. 236-255
    • Vieites, J.M.1    Guazzaroni, M.E.2    Beloqui, A.3    Golyshin, P.N.4    Ferrer, M.5
  • 23
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • 10.1186/gb-2009-10-3-r25, 2690996, 19261174
    • Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10(3):R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
    • (2009) Genome Biol , vol.10 , Issue.3
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 25
    • 75249099835 scopus 로고    scopus 로고
    • A white-box approach to microarray probe response characterization: the BaFL pipeline
    • 10.1186/1471-2105-10-449, 2804686, 20040098
    • Thompson KJ, Deshmukh H, Solka JL, Weller JW. A white-box approach to microarray probe response characterization: the BaFL pipeline. BMC Bioinformatics 2009, 10:449. 10.1186/1471-2105-10-449, 2804686, 20040098.
    • (2009) BMC Bioinformatics , vol.10 , pp. 449
    • Thompson, K.J.1    Deshmukh, H.2    Solka, J.L.3    Weller, J.W.4
  • 27
    • 50649089207 scopus 로고    scopus 로고
    • RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays
    • 10.1101/gr.079558.108, 2527709, 18550803
    • Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 2008, 18(9):1509-1517. 10.1101/gr.079558.108, 2527709, 18550803.
    • (2008) Genome Res , vol.18 , Issue.9 , pp. 1509-1517
    • Marioni, J.C.1    Mason, C.E.2    Mane, S.M.3    Stephens, M.4    Gilad, Y.5
  • 28
    • 0142121516 scopus 로고    scopus 로고
    • Exploration, normalization, and summaries of high density oligonucleotide array probe level data
    • 10.1093/biostatistics/4.2.249, 12925520
    • Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4(2):249-264. 10.1093/biostatistics/4.2.249, 12925520.
    • (2003) Biostatistics , vol.4 , Issue.2 , pp. 249-264
    • Irizarry, R.A.1    Hobbs, B.2    Collin, F.3    Beazer-Barclay, Y.D.4    Antonellis, K.J.5    Scherf, U.6    Speed, T.P.7
  • 29
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-Seq
    • 10.1038/nmeth.1226, 18516045
    • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5(7):621-628. 10.1038/nmeth.1226, 18516045.
    • (2008) Nat Methods , vol.5 , Issue.7 , pp. 621-628
    • Mortazavi, A.1    Williams, B.A.2    McCue, K.3    Schaeffer, L.4    Wold, B.5
  • 30
    • 0035923521 scopus 로고    scopus 로고
    • Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses
    • 10.1073/pnas.191502998, 61120, 11707567
    • Bhattacharjee A, Richards WG, Staunton J, Li C, Monti S, Vasa P, Ladd C, Beheshti J, Bueno R, Gillette M, et al. Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci USA 2001, 98(24):13790-13795. 10.1073/pnas.191502998, 61120, 11707567.
    • (2001) Proc Natl Acad Sci USA , vol.98 , Issue.24 , pp. 13790-13795
    • Bhattacharjee, A.1    Richards, W.G.2    Staunton, J.3    Li, C.4    Monti, S.5    Vasa, P.6    Ladd, C.7    Beheshti, J.8    Bueno, R.9    Gillette, M.10
  • 31
    • 33144462268 scopus 로고    scopus 로고
    • Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis
    • 10.1093/jnci/djj052, 16478745
    • Sotiriou C, Wirapati P, Loi S, Harris A, Fox S, Smeds J, Nordgren H, Farmer P, Praz V, Haibe-Kains B, et al. Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. J Natl Cancer Inst 2006, 98(4):262-272. 10.1093/jnci/djj052, 16478745.
    • (2006) J Natl Cancer Inst , vol.98 , Issue.4 , pp. 262-272
    • Sotiriou, C.1    Wirapati, P.2    Loi, S.3    Harris, A.4    Fox, S.5    Smeds, J.6    Nordgren, H.7    Farmer, P.8    Praz, V.9    Haibe-Kains, B.10
  • 32
    • 69849094662 scopus 로고    scopus 로고
    • AffyPara-a Bioconductor Package for Parallelized Preprocessing Algorithms of Affymetrix Microarray Data
    • 2808179, 20140068
    • Schmidberger M, Vicedo E, Mansmann U. affyPara-a Bioconductor Package for Parallelized Preprocessing Algorithms of Affymetrix Microarray Data. Bioinform Biol Insights 2009, 3:83-87. 2808179, 20140068.
    • (2009) Bioinform Biol Insights , vol.3 , pp. 83-87
    • Schmidberger, M.1    Vicedo, E.2    Mansmann, U.3
  • 33
    • 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
  • 34
    • 50649122770 scopus 로고    scopus 로고
    • EagleView: a genome assembly viewer for next-generation sequencing technologies
    • 10.1101/gr.076067.108, 2527701, 18550804
    • Huang W, Marth G. EagleView: a genome assembly viewer for next-generation sequencing technologies. Genome Res 2008, 18(9):1538-1543. 10.1101/gr.076067.108, 2527701, 18550804.
    • (2008) Genome Res , vol.18 , Issue.9 , pp. 1538-1543
    • Huang, W.1    Marth, G.2
  • 35
    • 0004053148 scopus 로고
    • The AWK programming language
    • Reading, Mass.: Addison-Wesley Pub. Co
    • Aho AV, Kernighan BW, Weinberger PJ. The AWK programming language. 1988, Reading, Mass.: Addison-Wesley Pub. Co.
    • (1988)
    • Aho, A.V.1    Kernighan, B.W.2    Weinberger, P.J.3
  • 38
    • 67349091736 scopus 로고    scopus 로고
    • Regulation of the extracellular antioxidant selenoprotein plasma glutathione peroxidase (GPx-3) in mammalian cells
    • 10.1007/s11010-009-0049-x, 2693281, 19219623
    • Ottaviano FG, Tang SS, Handy DE, Loscalzo J. Regulation of the extracellular antioxidant selenoprotein plasma glutathione peroxidase (GPx-3) in mammalian cells. Mol Cell Biochem 2009, 327(1-2):111-126. 10.1007/s11010-009-0049-x, 2693281, 19219623.
    • (2009) Mol Cell Biochem , vol.327 , Issue.1-2 , pp. 111-126
    • Ottaviano, F.G.1    Tang, S.S.2    Handy, D.E.3    Loscalzo, J.4
  • 39
    • 65949099336 scopus 로고    scopus 로고
    • A primary xenograft model of small-cell lung cancer reveals irreversible changes in gene expression imposed by culture in vitro
    • 10.1158/0008-5472.CAN-08-4210, 2821899, 19351829
    • Daniel VC, Marchionni L, Hierman JS, Rhodes JT, Devereux WL, Rudin CM, Yung R, Parmigiani G, Dorsch M, Peacock CD, et al. A primary xenograft model of small-cell lung cancer reveals irreversible changes in gene expression imposed by culture in vitro. Cancer Res 2009, 69(8):3364-3373. 10.1158/0008-5472.CAN-08-4210, 2821899, 19351829.
    • (2009) Cancer Res , vol.69 , Issue.8 , pp. 3364-3373
    • Daniel, V.C.1    Marchionni, L.2    Hierman, J.S.3    Rhodes, J.T.4    Devereux, W.L.5    Rudin, C.M.6    Yung, R.7    Parmigiani, G.8    Dorsch, M.9    Peacock, C.D.10
  • 40
    • 48249130774 scopus 로고    scopus 로고
    • At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana
    • 10.1186/gb-2008-9-7-r112, 2530869, 18613972
    • Laubinger S, Zeller G, Henz SR, Sachsenberg T, Widmer CK, Naouar N, Vuylsteke M, Scholkopf B, Ratsch G, Weigel D. At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana. Genome Biol 2008, 9(7):R112. 10.1186/gb-2008-9-7-r112, 2530869, 18613972.
    • (2008) Genome Biol , vol.9 , Issue.7
    • Laubinger, S.1    Zeller, G.2    Henz, S.R.3    Sachsenberg, T.4    Widmer, C.K.5    Naouar, N.6    Vuylsteke, M.7    Scholkopf, B.8    Ratsch, G.9    Weigel, D.10
  • 41
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genomewide studies
    • 10.1073/pnas.1530509100, 170937, 12883005
    • Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proc Natl Acad Sci USA 2003, 100(16):9440-9445. 10.1073/pnas.1530509100, 170937, 12883005.
    • (2003) Proc Natl Acad Sci USA , vol.100 , Issue.16 , pp. 9440-9445
    • Storey, J.D.1    Tibshirani, R.2
  • 42
    • 0034730140 scopus 로고    scopus 로고
    • Singular value decomposition for genome-wide expression data processing and modeling
    • 10.1073/pnas.97.18.10101, 27718, 10963673
    • Alter O, Brown PO, Botstein D. Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci USA 2000, 97(18):10101-10106. 10.1073/pnas.97.18.10101, 27718, 10963673.
    • (2000) Proc Natl Acad Sci USA , vol.97 , Issue.18 , pp. 10101-10106
    • Alter, O.1    Brown, P.O.2    Botstein, D.3
  • 43
    • 0347090327 scopus 로고    scopus 로고
    • Adjustment of systematic microarray data biases
    • 10.1093/bioinformatics/btg385, 14693816
    • Benito M, Parker J, Du Q, Wu J, Xiang D, Perou CM, Marron JS. Adjustment of systematic microarray data biases. Bioinformatics 2004, 20(1):105-114. 10.1093/bioinformatics/btg385, 14693816.
    • (2004) Bioinformatics , vol.20 , Issue.1 , pp. 105-114
    • Benito, M.1    Parker, J.2    Du, Q.3    Wu, J.4    Xiang, D.5    Perou, C.M.6    Marron, J.S.7
  • 44
    • 33845432928 scopus 로고    scopus 로고
    • Adjusting batch effects in microarray expression data using empirical Bayes methods
    • 10.1093/biostatistics/kxj037, 16632515
    • Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007, 8(1):118-127. 10.1093/biostatistics/kxj037, 16632515.
    • (2007) Biostatistics , vol.8 , Issue.1 , pp. 118-127
    • Johnson, W.E.1    Li, C.2    Rabinovic, A.3


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