Data storage and analysis in ArrayExpress and expression profiler

Current Protocols in Bioinformatics

Volumn , Issue SUPPL. 23, 2008, Pages

  Rustici, Gabriella ^a   Kapushesky, Misha ^a   Kolesniko, Nikolay ^a   Parkinson, Helen ^a   Sarkans, Ugis ^a   Brazma, Alvis ^a  

^a EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

Data analysis; Gene expression; Microarrays; Public repository; Transcriptomics

Indexed keywords

ARRAYEXPRESS; BIOINFORMATICS; CHROMOSOMAL LOCALIZATION; CLUSTER ANALYSIS; COMPUTER INTERFACE; COMPUTER PROGRAM; DATA ANALYSIS; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENETIC DATABASE; INFORMATION PROCESSING; INFORMATION RETRIEVAL; INTERNET; NOMENCLATURE; ONLINE ANALYSIS; PRIORITY JOURNAL; PROBABILITY; REVIEW; TRANSCRIPTOMICS; WEB BROWSER;

EID: 58749115963     PISSN: 19343396     EISSN: 1934340X     Source Type: Journal    
DOI: 10.1002/0471250953.bi0713s23     Document Type: Review

References (28)

1. Ashburner, M., Ball, C., Blake, J., Botstein, D., Butler, H., Cherry, J., Davis, A., Dolinski, K., Dwight, S., Eppig, J., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., and Sherlock, G. 2000. Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25:25-29.
2. Ball, C., Brazma, A., Causton, H., Chervitz, S., Edgar, R., Hingamp, P., Matese, J.C., Icahn, C., Parkinson, H., Quackenbush, J., Ringwald, M., Sansone, S.A., Sherlock, G., Spellman, P., Stoeckert, C., Tateno, Y., Taylor, R., White, J., and Winegarden, N. 2004. An open letter on microarray data from the MGED Society. Microbiology 150:3522-3524.
3. Benjamini, Y. and Hochberg, Y. 1995. Controlling the false discovery rate: Apractical and powerful approach to multiple testing. J. R. Stat. Soc. B 57:289-300.
4. Blake, J., Schwager, C., Kapushesky, M., and Brazma, A. 2006. ChroCoLoc: An application for calculating the probability of co-localization of microarray gene expression. Bioinformatics 22:765-767.
5. 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., and Vingron, M. 2001. Minimum information about a microarray experiment (MIAME)- toward standards for microarray data. Nat. Genet. 29:365-371.
6. 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., and Sansone, S.A. 2003. ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 31:68-71.
7. Culhane, A.C., Perriere, G., Considine, E.C., Cotter, T.G., and Higgins, D.G. 2002. Betweengroup analysis of microarray data. Bioinformatics 18:1600-1608.
8. Culhane, A.C., Thioulouse, J., Perriere, G., and Higgins, D.G. 2005. MADE4: An R package for multivariate analysis of gene expression data. Bioinformatics 21:2789-2790.
9. Edgar, R., Domrachev, M., and Lash, A.E. 2002. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30:207-210.
10. Hochberg,Y. 1988.Asharper Bonferroni procedure for multiple tests of significance. Biometrika 75:800-803.
11. Holm, S. 1979. A simple sequentially rejective Bonferroni test procedure. Scand. J. Stat. 6:65- 70.
12. Huber, W., von Heydebreck, A., Sultmann, H., Poustka, A., and Vingron, M. 2002. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18:S96-S104.
13. Ihaka, R. and Gentleman, R. 1996. R: A language for data analysis and graphics. J. Comput. Graph. Stat. 5:299-314.
14. Ihmels, J., Friedlander, G., Bergmann, S., Sarig, O., Ziv, Y., and Barkai, N. 2002. Revealing modular organization in the yeast transcriptional network. Nat. Genet. 31:370-377.
15. Ikeo, K., Ishi-i, J., Tamura, T., Gojobori, T., and Tateno, Y. 2003. CIBEX: Center for information biology gene expression database. C. R. Biol. 326:1079-1082.
16. Irizarry, R.A., Bolstad, B.M., Collin, F., Cope, L.M., Hobbs, B., and Speed, T.P. 2003. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31:e15.
17. Johansson, P. and Hakkinen, J. 2006. Improving missing value imputation of microarray data by using spot quality weights. BMC Bioinformatics 7:306.
18. Kapushesky, M., Kemmeren, P., Culhane, A.C., Durinck, S., Ihmels, J., Korner, C., Kull, M., Torrente, A., Sarkans, U., Vilo, J., and Brazma, A. 2004. Expression Profiler: Next generationan online platform for analysis of microarray data. Nucleic Acids Res. 32:W465- W470.
19. Li, C. and Wong, W.H. 2001. Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. Proc. Natl. Acad. Sci. U.S.A. 98:31-36.
20. Manly, K.F., Nettleton, D., and Hwang, J.T. 2004. Genomics, prior probability, and statistical tests of multiple hypotheses. Genome Res. 14:997- 1001.
21. Pounds, S. 2006. Estimation and control of multiple testing error rates for microarray studies. Brief. Bioinform. 7:25-36.
22. Quackenbush, J. 2001. Computational analysis of microarray data. Nat. Rev. Genet. 2:418- 427.
23. Quackenbush, J. 2002. Microarray data normalization and transformation. Nat. Genet. 32:496- 501.
24. Rayner, T.F., Rocca-Serra, P., Spellman, P.T., Causton, H.C., Farne, A., Holloway, E., Irizarry, R.A., Liu, J., Maier, D.S., Miller, M., Petersen, K., Quackenbush, J., Sherlock, G., Stoeckert, C.J., White, J., Whetzel, P.L., Wymore, F., Parkinson, H., Sarkans, U., Ball, C.A., and Brazma, A. 2006. A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics 7:489.
25. Smyth, G.K. 2004. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3:ARticle3.
26. Torrente, A., Kapushesky, M., and Brazma, A. 2005. A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings. Bioinformatics 21:3993-3999.
27. Troyanskaya, O., Cantor, M., Sherlock, G., Brown, P., Hastie, T., Tibshirani, R., Botstein, D., and Altman, R.B. 2001. Missing value estimation methods for DNA microarrays. Bioinformatics 17:520-525.
28. Wu, Z., Irizarry, R., Gentleman, R., Martinez- Murillo, F., and Spencer, F. 2004. A modelbased background adjustment for oligonucleotide expression arrays. J. Am. Stat. Assoc. 99:909-917.