THEME: A web tool for loop-design microarray data analysis

Computers in Biology and Medicine

Volumn 42, Issue 2, 2012, Pages 228-234

  Chen, Chaang Ray ^a   Shu, Wun Yi ^a   Tsai, Min Lung ^a   Cheng, Wei Chung ^a   Hsu, Ian C ^a  

^a NATIONAL TSING HUA UNIVERSITY   (Taiwan)

Author keywords

Bioinformatics; Differentially expressed genes; Linear models; Loop design; Microarray

Indexed keywords

COLLABORATION PROJECTS; DATA ANALYSIS TOOL; DATA ASSESSMENT; DESIGN MATRIX; DIFFERENTIALLY EXPRESSED GENE; EXPERIMENTAL PROCEDURE; FACILITY SERVICES; LOOP-DESIGN; MATRIX; MICROARRAY DATA ANALYSIS; MICROARRAY EXPERIMENTS; MINIMAL INFORMATION; RAW DATA FILES; REFERENCE CONTROL; SPECIALIZED KNOWLEDGE; VISUALIZATION TOOLS; WEB TOOLS; WEB-BASED RESOURCES; WEB-BASED TOOLS; WORK-FLOWS;

BIOINFORMATICS; DATA VISUALIZATION; DESIGN; EXPERIMENTS; GENE EXPRESSION; MATHEMATICAL MODELS; MICROARRAYS; STATISTICAL TESTS; STATISTICS; VISUALIZATION; WEB SERVICES;

DESIGN OF EXPERIMENTS;

ARTICLE; DATA ANALYSIS; EXPERIMENTAL DESIGN; GENE EXPRESSION; HUMAN; KNOWLEDGE; MICROARRAY ANALYSIS; PRIORITY JOURNAL; RELIABILITY; STATISTICAL MODEL; VALIDATION STUDY;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION PROFILING; INTERNET; LINEAR MODELS; MICROARRAY ANALYSIS; SOFTWARE;

EID: 84855924077     PISSN: 00104825     EISSN: 18790534     Source Type: Journal    
DOI: 10.1016/j.compbiomed.2011.11.012     Document Type: Article

References (37)

1. Churchill G.A. Fundamentals of experimental design for cDNA microarrays. Nat. Genet. 2002, 32(Suppl.):490-495.
2. Hutter S., Saminadin-Peter S.S., Stephan W., Parsch J. Gene expression variation in African and European populations of Drosophila melanogaster. Genome Biol. 2008, 9:R12.
3. Kerr M.K., Churchill G.A. Statistical design and the analysis of gene expression microarray data. Genet. Res. 2001, 77:123-128.
4. Kerr M.K., Churchill G.A. Experimental design for gene expression microarrays. Biostatistics 2001, 2:183-201.
5. Oleksiak M.F., Roach J.L., Crawford D.L. Natural variation in cardiac metabolism and gene expression in Fundulus heteroclitus. Nat. Genet. 2005, 37:67-72.
6. Townsend J.P. Multifactorial experimental design and the transitivity of ratios with spotted dna microarrays. BMC Genomics 2003, 4:41.
7. Whitehead A., Crawford D.L. Variation in tissue-specific gene expression among natural populations. Genome Biol. 2005, 6:R13.
8. Yang Y.H., Speed T. Design issues for cDNA microarray experiments. Nat. Rev. Genet. 2002, 3:579-588.
9. Clark T.A., Townsend J.P. Quantifying variation in gene expression. Mol. Ecol. 2007, 16:2613-2616.
10. Tempelman R.J. Assessing statistical precision, power, and robustness of alternative experimental designs for two color microarray platforms based on mixed effects models. Vet. Immunol. Immunop. 2005, 105:175-186.
11. Vinciotti V., Khanin R., D'Alimonte D., Liu X., Cattini N., Hotchkiss G., Bucca G., de Jesus O., Rasaiyaah J., Smith C.P., Kellam P., Wit E. An experimental evaluation of a loop versus a reference design for two-channel microarrays. Bioinformatics 2005, 21:492-501.
12. E. Wit, J. McClure, Statistical design of microarrays, in: Statistics for Microarrays: Design, Analysis and Inference, John Wiley & Sons, Chichester; Hoboken, NJ, 2004, pp. 23-56.
13. Smyth G.K. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 2004, 3. (Article3).
14. Quackenbush J. Microarray data normalization and transformation. Nat. Genet. 2002, 32:496-501. Suppl.
15. Smyth G.K. Limma: linear models for microarray data. Bioinformatics and Computational Biology Solutions using R and Bioconductor 2005, 397-420. Springer, NY. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (Eds.).
16. Wettenhall J.M., Smyth G.K. limmaGUI: a graphical user interface for linear modeling of microarray data. Bioinformatics 2004, 20:3705-3706.
17. Gentleman R.C., Carey V.J., Bates D.M., Bolstad B., Dettling M., Dudoit S., Ellis B., Gautier L., Ge Y., Gentry J., Hornik K., Hothorn T., Huber W., Iacus S., Irizarry R., Leisch F., Li C., Maechler M., Rossini A.J., Sawitzki G., Smith C., Smyth G., Tierney L., Yang J.Y., Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004, 5:R80.
18. Sherlock G., Hernandez-Boussard T., Kasarskis A., Binkley G., Matese J.C., Dwight S.S., Kaloper M., Weng S., Jin H., Ball C.A., Eisen M.B., Spellman P.T., Brown P.O., Botstein D., Cherry J.M. The Stanford microarray database. Nucleic Acids Res. 2001, 29:152-155.
19. Edgar R., Domrachev M., Lash A.E. Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002, 30:207-210.
20. Brazma A., Parkinson H., Sarkans U., Shojatalab M., Vilo J., Abeygunawardena N., Holloway E., Kapushesky M., Kemmeren P., Lara G.G., Oezcimen A., Rocca-Serra P., Sansone S.A. ArrayExpress-a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 2003, 31:68-71.
21. Brazma A., Hingamp P., Quackenbush J., Sherlock G., Spellman P., Stoeckert C., Aach J., Ansorge W., Ball C.A., Causton H.C., Gaasterland T., Glenisson P., Holstege F.C., Kim I.F., Markowitz V., Matese J.C., Parkinson H., Robinson A., Sarkans U., Schulze-Kremer S., Stewart J., Taylor R., Vilo J., Vingron M. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat. Genet. 2001, 29:365-371.
22. Hokamp K., Roche F.M., Acab M., Rousseau M.E., Kuo B., Goode D., Aeschliman D., Bryan J., Babiuk L.A., Hancock R.E., Brinkman F.S. ArrayPipe: a flexible processing pipeline for microarray data. Nucleic Acids Res. 2004, 32:W457-W459.
23. Killion P.J., Sherlock G., Iyer V.R. The longhorn array database (LAD): an open-source, MIAME compliant implementation of the Stanford microarray database (SMD). BMC Bioinformatics 2003, 4:32.
24. Herrero J., Al-Shahrour F., Diaz-Uriarte R., Mateos A., Vaquerizas J.M., Santoyo J., Dopazo J. GEPAS: a web-based resource for microarray gene expression data analysis. Nucleic Acids Res. 2003, 31:3461-3467.
25. Saal L.H., Troein C., Vallon-Christersson J., Gruvberger S., Borg A., Peterson C. BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data. Genome Biol. 2002, 3. SOFTWARE0003.
26. Rainer J., Sanchez-Cabo F., Stocker G., Sturn A., Trajanoski Z. CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis. Nucleic Acids Res. 2006, 34:W498-W503.
27. Xia X., McClelland M., Wang Y. WebArray: an online platform for microarray data analysis. BMC Bioinformatics 2005, 6:306.
28. Argraves G.L., Jani S., Barth J.L., Argraves W.S. ArrayQuest: a web resource for the analysis of DNA microarray data. BMC Bioinformatics 2005, 6:287.
29. Maurer M., Molidor R., Sturn A., Hartler J., Hackl H., Stocker G., Prokesch A., Scheideler M., Trajanoski Z. MARS: microarray analysis, retrieval, and storage system. BMC Bioinformatics 2005, 6:101.
30. Greer K.A., McReynolds M.R., Brooks H.L., Hoying J.B. CARMA: a platform for analyzing microarray datasets that incorporate replicate measures. BMC Bioinformatics 2006, 7:149.
31. Romualdi C., Vitulo N., Del Favero M., Lanfranchi G. MIDAW: a web tool for statistical analysis of microarray data. Nucleic Acids Res. 2005, 33:W644-W649.
32. Yang Y.H., Dudoit S., Luu P., Lin D.M., Peng V., Ngai J., Speed T.P. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 2002, 30:e15.
33. Yang I.V., Chen E., Hasseman J.P., Liang W., Frank B.C., Wang S., Sharov V., Saeed A.I., White J., Li J., Lee N.H., Yeatman T.J., Quackenbush J. Within the fold: assessing differential expression measures and reproducibility in microarray assays. Genome Biol. 2002, 3. (research0062).
34. Benjamini Y., Hochberg Y. Controlling the false discovery rate-a practical and powerful approach to multiple testing. J. Roy. Stat. Soc. B Met 1995, 57:289-300.
35. Tsai M.L., Chang K.Y., Chiang C.S., Shu W.Y., Weng T.C., Chen C.R., Huang C.L., Lin H.K., Hsu I.C. UVB radiation induces persistent activation of ribosome and oxidative phosphorylation pathways. Radiat. Res. 2009, 171:716-724.
36. Huang C.L., Shu W.Y., Tsai M.L., Chiang C.S., Chang C.W., Chang C.T., Hsu I.C. Repeated small perturbation approach reveals transcriptomic steady states. PLoS ONE 2011, 6(12):e29241. 10.1371/journal.pone.0029241.
37. W.C. Cheng, W.Y. Shu, C.Y. Li, M.L. Tsai, C.W. Chang, C.R. Chen, H.T. Cheng, T.H. Wang, I.C. Hsu, Intra- and inter-individual variance of gene expression in clinical studies, PLoS ONE, submitted for publication.