Improving identification of differentially expressed genes by integrative analysis of Affymetrix and illumina arrays

OMICS A Journal of Integrative Biology

Volumn 10, Issue 3, 2006, Pages 369-380

  Elo, Laura L ^a,b   Katajamaa, Mikko ^b   Lund, Riikka ^b   Orešič, Matej ^b,c   Lahesmaa, Riitta ^b   Aittokallio, Tero ^a,b,d  

^a UNIVERSITY OF TURKU   (Finland)

^b TURKU CENTRE FOR BIOTECHNOLOGY   (Finland)

^c VTT TECHNICAL RESEARCH CENTRE OF FINLAND   (Finland)

^d INSTITUT PASTEUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; CELL DIFFERENTIATION; COST EFFECTIVENESS ANALYSIS; GENE EXPRESSION; GENE IDENTIFICATION; GENOME ANALYSIS; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; PRIORITY JOURNAL; REPRODUCIBILITY; TH2 CELL;

CELL DIFFERENTIATION; CELLS, CULTURED; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; TH2 CELLS;

EID: 33750933836     PISSN: 15362310     EISSN: None     Source Type: Journal    
DOI: 10.1089/omi.2006.10.369     Document Type: Article

References (27)

1. ASHBURNER, M., BALL, C.A., BLAKE, J.A., et al. (2000). Gene ontology: tool for the unification of biology. Nat Genet 25, 25-29.
2. BARNES, M., FREUDENBERG, J., THOMPSON, S., et al. (2005). Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms. Nucleic Acids Res 33, 5914-5923.
3. BOLSTAD, B.M., IRIZARRY, R.A., ASTRAND, M., et al. (2003). A comparison of normalization methods for high-density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185-193.
4. CHOI, J.K., YU, U., KIM, S., et al. (2003). Combining multiple microarray studies and modeling interstudy variation. Bioinformatics 19, i84-i90.
5. DAI, M., WANG, P., BOYD, A.D., et al. (2005). Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res 33, e175.
6. EFRON, B., TIBSHIRANI, R., STOREY, J.D., et al. (2001). Empirical Bayes analysis of a microarray experiment. J Am Stat Assoc 96, 1151-1160.
7. ELO, L.L., LAHTI, L., SKOTTMAN, H., et al. (2005). Integrating probe-level expression changes across generations of Affymetrix arrays. Nucleic Acids Res 33, e193.
8. ELSER, B., LOHOFF, M., KOCK, S., et al. (2002). IFN-gamma represses IL-4 expression via IRF-1 and IRF-2. Immunity 17, 703-712.
9. GENTLEMAN, R.C., CAREY, V.J., BATES, D.M., et al. (2004). Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5, R80.
10. GENTLEMAN, R., SCHOLTENS, D., DING, B., et al. (2005). Case studies using graphs on biological data. In: Gentleman, R., Carey, V.J. Huber, W., et al., eds. Bioinformatics and Computational Biology Solutions Using R and Bioconductor (Springer, New York), pp. 369-394.
11. GUNDERSON, K.L., KRUGLYAK, S., GRAIGE, M.S., et al. (2004). Decoding randomly ordered DNA arrays. Genome Res 14, 870-877.
12. HEDGES, L.V., and OLKIN, I. (1985). Statistical Methods for Meta-Analysis (Academic Press, Orlando, FL).
13. HÄMÄLÄINEN, H., MEISSNER, S., and LAHESMAA, R. (2000). Signaling lymphocytic activation molecule (SLAM) is differentially expressed in human Th1 and Th2 cells. J Immunol Methods 242, 9-19.
14. IRIZARRY, R.A., HOBBS, B., COLLIN, F., et al. (2003). Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4, 249-264.
15. IRIZARRY, R.A., WARREN, D., SPENCER, F., et al. (2005). Multiple-laboratory comparison of microarray platforms. Nat Methods 2, 345-350.
16. JOURDAN, P., ABBAL, C., NORAZ, N., et al. (1998). IL-4 induces functional cell-surface expression of CXCR4 on human T cells. J Immunol 160, 4153-4157.
17. LOCKHART, D.J., DONG, H., BYRNE, M.C., et al. (1996). Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 14, 1675-1680.
18. + lymphocytes. J Immunol 171, 5328-5336.
19. LUND, R. (2004). Identification of novel genes involved in the early differentiation of Th1 and Th2 cells [Ph.D. dissertation]. Turku, Finland: University of Turku.
20. LUND, R., AHLFORS, H., KAINONEN, E., et al. (2005). Identification of genes involved in the initiation of human Th1 or Th2 cell commitment. Eur J Immunol 35, 3307-3319.
21. MECHAM, B.H., KLUS, G.T., STROVEL, J., et al. (2004). Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. Nucleic Acids Res 32, e74.
22. MOWEN, K.A., and GLIMCHER, L.H. (2004). Signaling pathways in Th2 development. Immunol Rev 202, 203-222.
23. MUKHERJEE, S., ROBERTS, S.J., and VAN DER LAAN, MJ. (2005). Data-adaptive test statistics for microarray data. Bioinformatics 21, ii108-ii114.
24. ROGGE, L., BIANCHI, E., BIFFI, M., et al. (2000). Transcript imaging of the development of human T helper cells using oligonucleotide arrays. Nat Genet 25, 96-101.
25. SHI, L., TONG, W., FANG, H., et al. (2005). Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential. BMC Bioinformatics 6, S12.
26. SMYTH, G.K. (2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3, 3.
27. TUSHER, V.G., TIBSHIRANI, R., and CHU, G. (2001). Significance analysis of microarrays applied to ionizing radiation response. Proc Natl Acad Sci USA 98, 5116-5121.