Identifying differentially expressed genes in the absence of replication

International Journal of Bioinformatics Research and Applications

Volumn 9, Issue 1, 2013, Pages 71-90

  Thilakarathne, Pushpike J ^a,b   Verbeke, Geert ^a,b   Engelen, Kristof ^c   Marchal, Kathleen ^c   Lin, Dan ^a,b  

^a UNIVERSITY OF LEUVEN   (Belgium)

^b HASSELT UNIVERSITY   (Belgium)

^c Centre of Microbial and Plant Genetics   (Belgium)

Author keywords

cDNA; Linear mixed effects model; Microarray data analysis; Standardised conditional residuals

Indexed keywords

EID: 84870696904     PISSN: 17445485     EISSN: 17445493     Source Type: Journal    
DOI: 10.1504/IJBRA.2013.050654     Document Type: Conference Paper

References (30)

1. Baldi, P. and Long, A. (2001) 'A Bayesian framework for the analysis of microarray expression data: regularised t-test and statistical inference of gene changes', Bioinformatics, Vol. 17, pp.509-19. (Pubitemid 32600497)
2. Benjamini, Y. and Hochberg, Y. (1995) 'Controlling the false discovery rate: a practical and powerful approach to multiple testing', Journal of the Royal Statistical Society Series B, Vol. 57, pp.289-300.
3. Bowtell, D. and Sambrook, J. (2003) DNA Microarrays: A Molecular Cloning Manual, NY Cold Spring Harbor Press, Cold Spring.
4. Callow, M., Dudoit, S., Gong, E., Speed, T. and Rubin, E. (2000) 'Microarray expression profiling identifies genes with altered expression in hdl-defeficient mice', Genome Research, Vol. 10, pp.2022-2029. (Pubitemid 32049146)
5. Chu, T., Weir, B. and Wolfinger, R. (2002) 'A systematic statistical linear modeling approach to oligonucleotide array experiments', Math. Biosci., Vol. 176, pp.35-51. (Pubitemid 34242098)
6. Cui, X. and Churchill, G. (2003) 'Statistical tests for differential expression in cDNA microarray experiments', Genome Biology, Vol. 4, pp.210.1-210.10.
7. DeRisi, J., Penland, L., Brown, P., Bittner, M., Meltzer, P., Ray, M., Chen, Y., Su, Y. and Trent, J. (1996) 'Use of a cDNA microarray to analyse gene expression patterns in human cancer', Nature Genetics, Vol. 14, pp.457-460. (Pubitemid 26414590)
8. Drǎghici, S. (Ed.) (2003) Data Analysis Tools for DNA Microarrays, Chapman & Hall/CRC, London.
9. Dudoit, S., Yang, Y., Speed, T. and Callow, M. (2002) 'Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments', Statistica Sinica, Vol. 12, pp.111-39.
10. Efron, E., Tibshirani, R., Storey, J. and Tusher, V. (2001) 'Empirical bayes analysis of a microarray experiment', Journal of the American Statistical Association, Vol. 96, pp.1151-1160. (Pubitemid 33695570)
11. Henderson, C. (1975) 'Best linear unbiased estimation and prediction under a selection model', Biometrics, Vol. 31, No. 2, pp.423-447.
12. Hilson, P., Allemeersch, J., Altmann, T., Aubourg, S., Avon, A. and Beynon, J. (2004) 'Versatile gene-specific sequence tags for arabidopsis functional genomics: 145 bibliography transcript profiling and reverse genetics applications', Biometrics, Vol. 14, pp.2176-2189. (Pubitemid 39440201)
13. Jin, W., Riley, R., Wolfinger, R., White, K., Passador-Gurgel, G., and Gibson, G. (2001) 'The contributions of sex, genotype and age to transcriptional variance in drosophila melanogaster', Nature Genetics, Vol. 29, pp.389-395. (Pubitemid 34326688)
14. Kerr, M., Martin, M. and Churchill, G. (2000) 'Analysis of variance for gene expression microarray data', Journal of Computational Biology, Vol. 7, pp.819-837.
15. Lockhart, D., Dong, H., Byrne, M., Follettie, M., Gallo, M., Chee, M., Mittermann, M., Wang, C., Kobayashi, M., Horton, H. and Brown, E. (1996) 'Expression monitoring by hybridisation to high-density oligonucleotide arrays', Nature Biotechnology, Vol. 14, pp.1675-1680. (Pubitemid 26414810)
16. Lange, N. and Ryan, L. (1989) 'Assessing normality in random effects models', The Annals of Statistics, Vol. 17, pp.624-642.
17. Peeters, P.J., Göhlmann, H.W., Van den Wyngaert, I., Swagemakers, S.M., Bijnens, L., Kass, S.U. and Steckler, T. (2004) 'Transcriptional response to corticotropin-releasing factor in AtT-20 Cells', Molecular Pharmacology, Vol. 66, No. 5, pp.1083-1092. (Pubitemid 39411049)
18. Robinson, G. (1991) 'That blup is a good thing: the estimation of random effects', Statistical Science, Vol. 6, pp.15-51.
19. Schena, M. (2000) Microarray Biochip Technology, Biotechniques Books, NATICK, MA Eaton.
20. Schena, M., Shalon, D., Heller, R., Chai, A., Brown, P. and Davis, R.W. (1996) 'Parallel human genome analysis: microarray-based expression monitoring of 1000 genes', Proc. Natl. Acad. Sci. USA, Vol. 93, pp.10614-10619. (Pubitemid 26333036)
21. Smets, B., Snijder, P., Engelen, K., Joossens, E., Ghillebert, R., Thevissen, K., Marchal, K. and Winderickx, J. (2008) 'Genome-wide expression analysis reveals TORC1-dependent and independent functions of Sch9', FEMS Yeast Research, Vol. 8, pp.1276-1288.
22. Speed, T. (Ed.) (2003) Statistical Analysis of Gene Expression Microarray Data, Chapman & Hall/CRC, New York.
23. Thilakarathne, P.J., Verbeke, G., Engelen, K. and Marchal, K. (2009) 'A nonlinear mixed-effects model for estimating calibration intervals for unknown concentrations in two-colour microarray data with spike-ins', Stat Appl Genet Mol Biol., Vol. 8, No. 1, Article 5.
24. Thomas, J., Olson, J., Tapscott, S. and Zhao, L. (2001) 'An efficient and robust statitical modelling approach to discover differentally expressed genes using genomic expression profiles', Statistical Science, Vol. 11, pp.1227-1236. (Pubitemid 32677297)
25. Tusher, V., Tibshirani, R. and Chu, G. (2001) 'Significance analysis of microarrays applied to the ionising radiation response', Proc. Natl. Acad. Sci. USA, Vol. 98, No. 9, pp.5116-5121. (Pubitemid 32397092)
26. Verbeke, G. and Molenberghs, G. (2000) Linear Mixed Models for Longitudinal Data, Springer-Verlag, Springer Series in Statistics, New York.
27. Verbeke, G. and Lesaffre, E. (1997) 'The effect of misspecifying the random effects distribution in linear mixed models for longitudinal data', Computational Statistics and Data Analysis, Vol. 23, pp.541-556.
28. Wang, L., Zhang, B., Wolfinger, R. and Chen, X. (2008) 'An integrated approach for the analysis of biological pathways using mixed models', PLoS Genet., Vol. 4, p.e1000115.
29. Wolfinger, R., Gibson, G., Wolfinger, E., Bennett, L., Hamadeh, H., Bushel, P., Afshari, C. and Paules, R. (2001) 'Assessing gene significance from cDNA microarray expression data via mixed models', Journal of Computational Biology, Vol. 8, pp.625-638.
30. Wout, v.A., Lehrma, G., Mikheeva, S., O'Keeffe, G., Katze, M., Bumgarner, R., Geiss, G. and Mullins, J. (2003) 'Cellular gene expression upon human immunodeficiency virus type 1 infection of CD4+-T-cell line', Journal of Virology, Vol. 77, pp.1392-1402. (Pubitemid 36055561)