MMBGX: A method for estimating expression at the isoform level and detecting differential splicing using whole-transcript Affymetrix arrays

Nucleic Acids Research

Volumn 38, Issue 1, 2009, Pages

  Turro, Ernest ^a   Lewin, Alex ^a   Rose, Anna ^a   Dallman, Margaret J ^a   Richardson, Sylvia ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ACETYLSALICYLIC ACID;

ARTICLE; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; DNA MICROARRAY; EXON; GENE EXPRESSION; GENETIC ALGORITHM; HYBRIDIZATION; INTERMETHOD COMPARISON; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SPLICING; STATISTICAL ANALYSIS; VALIDATION PROCESS;

ALTERNATIVE SPLICING; ANIMALS; BAYES THEOREM; COLONIC NEOPLASMS; EXONS; GENE EXPRESSION PROFILING; HUMANS; MALE; MICE; MICE, INBRED C57BL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEIN ISOFORMS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SOFTWARE;

EID: 75649121097     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp853     Document Type: Article

References (24)

1. Naef, F. and Magnasco, M.O. (2003) Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays. Phys. Rev. E Stat. Nonlin. Soft Matter Phys., 68(Pt 1), 011906.
2. Wu, Z., Irizarry, R.A., Gentleman, R., Martinez-Murillo, F. and Spencer, F. (2004) A model-based background adjustment for oligonucleotide expression arrays. J. Am. Stat. Assoc., 99, 909-917.
3. Turro, E., Bochkina, N., Hein, A. and Richardson, S. (2007) BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips. BMC Bioinformatics, 8, 439.
4. Affymetrix, Inc. (2005) Affymetrix GeneChip Exon Array Design. Technical report, http://www.affymetrix.com/support/technical/technotes/exon_array_design_technote.pdf.
5. Affymetrix, Inc. (2005) Affymetrix Guide to Probe Logarithmic Intensity Error (PLIER) Estimation. Technical report, http://www.affymetrix.com/support/technical/technotes/plier_technote.pdf.
6. Affymetrix Inc. (2005) Affymetrix Exon Array Background Correction. Technical report, http://www.affymetrix.com/support/technical/whitepapers/exon_background_correction_whitepaper.pdf.
7. Clark, T.A., Schweitzer, A.C., Chen, T.X., Staples, M.K., Lu, G., Wang, H., Williams, A. and Blume, J.E. (2007) Discovery of tissue-specific exons using comprehensive human exon microarrays. Genome Biol., 8, R64.
8. Affymetrix Inc. (2005) Affymetrix Alternative Transcript Analysis Methods for Exon Arrays. Technical report, http://www.affymetrix.com/support/technical/whitepapers/exon_alt_transcript_analysis_whitepaper.pdf.
9. Purdom, E., Simpson, K.M., Robinson, M.D., Conboy, J.G., Lapuk, A.V. and Speed, T.P. (2008) FIRMA: a method for detection of alternative splicing from exon array data. Bioinformatics, 24, 1707-1714.
10. Frigessi, A., van deWiel, M.A., Holden, M., Svendsrud, D.H., Glad, I.K. and Lyng, H. (2005) Genome-wide estimation of transcript concentrations from spotted cDNA microarray data. Nucleic Acids Res, 33, e143.
11. Hein, A.-M.K., Richardson, S., Causton, H.C., Ambler, G.K. and Green, P.J. (2005) BGX: a fully Bayesian integrated approach to the analysis of Affymetrix GeneChip data. Biostatistics, 6, 349-373.
12. Flicek, P., Aken, B.L., Beal, K., Ballester, B., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cunningham, F., Cutts, T. et al. (2008) Ensembl 2008. Nucleic Acids Res, 36, D707-D714.
13. Hein, A.-M.K. and Richardson, S. (2006) A powerful method for detecting differentially expressed genes from genechip arrays that does not require replicates. BMC Bioinformatics, 7, 353.
14. Roberts, G.O. and Rosenthal, J.S. (2006) Examples of Adaptive MCMC, http://www.probability.ca/jeff/ftpdir/adaptex.pdf.
15. Yates, T., Okoniewski, M.J. and Miller, C.J. (2008) X:map: annotation and visualization of genome structure for Affymetrix exon array analysis. Nucleic Acids Res, 36, D780-D786.
16. Bolstad, B.M., Irizarry, R.A., Astrand, M. and Speed, T.P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics, 19, 185-193.
17. Irizarry, R.A., Hobbs, B., Collin, F., Beazer-Barclay, Y.D., Antonellis, K.J., Scherf, U. and Speed, T.P. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4, 249-264.
18. Gardina, P.J., Clark, T.A., Shimada, B., Staples, M.K., Yang, Q., Veitch, J., Schweitzer, A., Awad, T., Sugnet, C. and Dee, S. (2006) Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array. BMC Genomics, 7, 325.
19. Gaidatzis, D., Jacobeit, K., Oakeley, E.J. and Stadler, M.B. (2009) Overestimation of alternative splicing caused by variable probe characteristics in exon arrays. Nucleic Acids Res., 10.1093/nar/gkp508 [Epub ahead of print].
20. Storey, J.D. (2002) A direct approach to false discovery rates. J. Roy. Stat. Soc. Ser. B (Stat. Methodol.), 64, 479-498.
21. Shai, O., Morris, Q.D., Blencowe, B.J. and Frey, B.J. (2006) Inferring global levels of alternative splicing isoforms using a generative model of microarray data. Bioinformatics, 22, 606-613.
22. Wang, H., Hubbell, E., Hu, J.-S., Mei, G., Cline, M., Lu, G., Clark, T., Siani-Rose, M.A., Ares, M., Kulp, D.C. et al. (2003) Gene structurebased splice variant deconvolution using a microarray platform. Bioinformatics, 19(Suppl 1), i315-i322.
23. Zheng, S. and Chen, L. (2009) A hierarchical bayesian model for comparing transcriptomes at the individual transcript isoform level. Nucleic Acids Res, 37, e75.
24. Garcia-Blanco, M.A., Baraniak, A.P. and Lasda, E.L. (2004) Alternative splicing in disease and therapy. Nat. Biotechnol., 22, 535-546.