Cyber-T web server: Differential analysis of high-throughput data

Nucleic Acids Research

Volumn 40, Issue W1, 2012, Pages

  Kayala, Matthew A ^a   Baldi, Pierre ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYSIS OF VARIANCE; ARTICLE; BAYES THEOREM; BIOTRANSFORMATION; CLIENT SERVER APPLICATION; COMPUTER PROGRAM; DOCUMENTATION; HIGH THROUGHPUT SCREENING; MATHEMATICAL ANALYSIS; PLOTS AND CURVES; PRIORITY JOURNAL; PROBABILITY; STATISTICAL ANALYSIS; STATISTICAL SIGNIFICANCE; STUDENT T TEST; VARIANCE STABILIZING NORMALIZATION; WEB BROWSER;

BAYES THEOREM; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INTERNET; MASS SPECTROMETRY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEIN ARRAY ANALYSIS; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 84864427352     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks420     Document Type: Article

References (29)

1. Allison, D.B., Cui, X., Page, G.P. and Sabripour, M. (2006) Microarray data analysis: from disarray to consolidation and consensus. Nat. Rev. Genet., 7, 55-65.
2. Miron, M. and Nadon, R. (2006) Inferential literacy for experimental high-throughput biology. Trends Genet., 22, 84-89.
3. Baldi, P. and Long, A.D. (2001) A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics, 17, 509-519.
4. Huber, W., von Heydebreck, A., Sültmann, H., Poustka, A. and Vingron, M. (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics., 18(Suppl. 1), 96-104.
5. Sundaresh, S., Doolan, D.L., Hirst, S., Mu, Y., Unal, B., Davies, D.H., Felgner, P.L. and Baldi, P. (2006) Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques. Bioinformatics, 22, 1760-1766.
6. Crompton, P.D., Kayala, M.A., Traore, B., Kayentao, K., Ongoiba, A., Weiss, G.E., Molina, D.R., Burk, C., Waisberg, M., Jasinskas, A. et al. (2010) A prospective analysis of the Ab response to Plasmodium falciparum before and after a malaria season by protein microarray. Proc. Natl Acad. Sci. USA, 107, 6958-6963.
7. Kaake, R.M., Wang, X. and Huang, L. (2010) Profiling of protein interaction networks of protein complexes using affinity purification and quantitative mass spectrometry. Mol. Cell Proteomics, 9, 1650-1665.
8. Parkhomchuk, D., Borodina, T., Amstislavskiy, V., Banaru, M., Hallen, L., Krobitsch, S., Lehrach, H. and Soldatov, A. (2009) Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res., 37, e123.
9. Trapnell, C., Williams, B., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M.J., Salzberg, S.L., Wold, B.J. and Pachter, L. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol., 28, 511-515.
10. Robinson, M.D., McCarthy, D.J. and Smyth, G.K. (2010) Edger: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26, 139-140.
11. Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biol., 11, R106.
12. Efron, B., Tibshirani, R., Storey, J. and Tusher, V. (2001) Empirical Bayes analysis of a microarray experiment. J. Am. Stat. Assoc., 96, 1151-1160.
13. Smyth, G.K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stats. Appl. Genet. Mol. Biol., 3.
14. Ishwaran, H., Rao, J.S. and Kogalur, U.B. (2006) BAMarraytrade mark: Java software for Bayesian analysis of variance for microarray data. BMC Bioinformatics, 7, 59.
15. Morrissey, E.R. and Diaz-Uriarte, R. (2009) Pomelo II: finding differentially expressed genes. Nucleic Acids Res., 37, W581-W586.
16. Rainer, J., Sanchez-Cabo, F., Stocker, G., Sturn, A. and Trajanoski, Z. (2006) CARMAweb: comprehensive R-and bioconductor-based web service for microarray data analysis. Nucleic Acids Res., 34, W498-W503.
17. Choe, S.E., Boutros, M., Michelson, A.M., Church, G.M. and Halfon, M.S. (2005) Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol., 6, R16.
18. Murie, C., Woody, O., Lee, A.Y. and Nadon, R. (2009) Comparison of small n statistical tests of differential expression applied to microarrays. BMC Bioinformatics, 10, 45.
19. Dondrup, M., Hüser, A.T., Mertens, D. and Goesmann, A. (2009) An evaluation framework for statistical tests on microarray data. J. Biotechnol., 140, 18-26.
20. Zhu, Q., Miecznikowski, J.C. and Halfon, M.S. (2010) Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset. BMC Bioinformatics, 11, 285.
21. Bohnert, R. and Rätsch, G. (2010) rQuant.web: a tool for RNA-Seq-based transcript quantitation. Nucleic Acids Res., 38, W348-W351.
22. Friedman, B.A. and Maniatis, T. (2011) ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data. Genome Biol., 12, R69.
23. Goecks, J., Nekrutenko, A. and Taylor, J. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11, R86.
24. Rocke, D.M. and Durbin, B. (2003) Approximate variance-stabilizing transformations for gene-expression microarray data. Bioinformatics, 19, 966-972.
25. Dudoit, S., Shaffer, J.P. and Boldrick, J.C. (2003) Multiple hypothesis testing in microarray experiments. Stat. Sci., 18, 71-103.
26. Allison, D.B., Gadbury, G.L., Heo, M., Fernandez, J.R., Lee, C.-K., Prolla, T.A. and Weindruch, R. (2002) A mixture model approach for the analysis of microarray gene expression data. Comput. Stat. Data Anol., 39, 1-20.
27. Hung, S.P., Baldi, P. and Hatfield, G.W. (2002) Global Gene Expression Profiling in Escherichia coli K12. The effects of leucine-responsive regulatory protein. J. Biol. Chem., 277, 40309-40323.
28. Scheffé, H. (1959) The Analysis of Variance. Wiley, New York, NY, pp. 66-77.
29. The ENCODE (ENCyclopedia Of DNA Elements) Project. (2004) Science 306, 636-640.