Quality indicators increase the reliability of microarray data

Genomics

Volumn 80, Issue 4, 2002, Pages 385-394

  Raffelsberger, Wolfgang ^a   Dembélé, Doulaye ^a   Neubauer, Mike G ^b   Gottardis, Marco M ^b   Gronemeyer, Hinrich ^a  

^a INSTITUT DE GÉNÉTIQUE ET DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

^b BRISTOL MYERS SQUIBB PHARMACEUTICAL RESEARCH INSTITUTE   (United States)

Author keywords

Biostatistics; Cell differentiation; Gene expression profiling; Retinoic acid

Indexed keywords

RETINOIC ACID;

APOPTOSIS; ARTICLE; CELL DIFFERENTIATION; DNA MICROARRAY; GENE ACTIVATION; GENE CONTROL; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; INFORMATION PROCESSING; METABOLISM; ONCOGENE MYC; PRIORITY JOURNAL; PROMYELOCYTE; RELIABILITY;

ATRA;

EID: 0036421465     PISSN: 08887543     EISSN: None     Source Type: Journal    
DOI: 10.1006/geno.2002.6848     Document Type: Article

References (45)

1. Harrington, C. A., Rosenow, C., and Retief, J. (2000). Monitoring gene expression using DNA microarrays. Curr. Opin. Microbiol. 3: 285-291.
2. Lipshutz, R. J., Fodor, S. P., Gingeras, T. R., and Lockhart, D. J. (1999). High density synthetic oligonucleotide arrays. Nat. Genet. 21: 20-24.
3. Brown, P. O., and Botstein, D. (1999). Exploring the new world of the genome with DNA microarrays. Nat. Genet. 21: 33-37.
4. Eisen, M. B., Spellman, P. T., Brown, P. O., and Botstein, D. (1998). Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95: 14863-14868.
5. Tamayo, P., et al. (1999). Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation. Proc. Natl. Acad. Sci. USA 96: 2907-2912.
6. Brazma, A., and Vilo, J. (2000). Gene expression data analysis. FEBS Lett. 480: 17-24.
7. Quackenbush, J. (2001). Computational analysis of microarray data. Nat. Rev. Genet. 2: 418-427.
8. Cooper, C. S. (2001). Applications of microarray technology in breast cancer research. Breast Cancer Res. 3: 158-175.
9. Devaux, F., Marc, P., and Jacq, C. (2001). Transcriptomes, transcription activators and microarrays. FEBS Lett. 498: 140-144.
10. Alizadeh, A. A., Ross, D. T., Perou, C. M., and van de Rijn, M. (2001). Towards a novel classification of human malignancies based on gene expression patterns. J. Pathol. 195: 41-52.
11. Wang, X., Ghosh, S., and Guo, S. W. (2001). Quantitative quality control in microarray image processing and data acquisition. Nucleic Acids Res. 29: E75.
12. Yang, M. C., et al. (2001). A statistical method for flagging weak spots improves normalization and ratio estimates in microarrays. Physiol. Genomics 7: 45-53.
13. Lee, M. L., Kuo, F. C., Whitmore, G. A., and Sklar, J. (2000). Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations. Proc. Natl. Acad. Sci. USA 97: 9834-9839.
14. Tseng, G. C., Oh, M. K., Rohlin, L., Liao, J. C., and Wong, W. H. (2001). Issues in cDNA microarray analysis: Quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res. 29: 2549-2557.
15. Wildsmith, S. E., Archer, G. E., Winkley, A. J., Lane, P. W., and Bugelski, P. J. (2001). Maximization of signal derived from cDNA microarrays. Biotechniques 30: 202-206, 208.
16. Benoit, G. R., Tong, J. H., Balajthy, Z., and Lanotte, M. (2001). Exploring (novel) gene expression during retinoid-induced maturation and cell death of acute promyelocytic leukemia. Semin. Hematol. 38: 71-85.
17. Kastner, P., and Chan, S. (2001). Function of RARα during the maturation of neutrophils. Oncogene 20: 7178-7185.
18. Melnick, A., and Licht, J. D. (1999). Deconstructing a disease: RARα, its fusion partners, and their roles in the pathogenesis of acute promyelocytic leukemia. Blood 93: 3167-3215.
19. Pandolfi, P. P. (2001). Oncogenes and tumor suppressors in the molecular pathogenesis of acute promyelocytic leukemia. Hum. Mol. Genet. 10: 769-775.
20. Ruchaud, S., et al. (1994). Two distinctly regulated events, priming and triggering, during retinoid-induced maturation and resistance of NB4 promyelocytic leukemia cell line. Proc. Natl. Acad. Sci. USA 91: 8428-8432.
21. Altucci, L., et al. (2001). Retinoic acid-induced apoptosis in leukemia cells is mediated by paracrine action of tumor-selective death ligand TRAIL. Nat. Med. 7: 680-686.
22. Benoit, G., et al. (1999). RAR-independent RXR signaling induces t(15;17) leukemia cell maturation. EMBO J. 18: 7011-7018.
23. Liu, T. X., et al. (2000). Gene expression networks underlying retinoic acid-induced differentiation of acute promyelocytic leukemia cells. Blood 96: 1496-1504.
24. Leemans, R., et al. (2000). Quantitative transcript imaging in normal and heat-shocked Drosophila embryos by using high-density oligonucleotide arrays. Proc. Natl. Acad. Sci. USA 97: 12138-12143.
25. Taniguchi, M., Miura, K., Iwao, H., and Yamanaka, S. (2001). Quantitative assessment of DNA microarrays - Comparison with northern blot analyses. Genomics 71: 34-39.
26. Kelly, D. L., and Rizzino, A. (2000). DNA microarray analyses of genes regulated during the differentiation of embryonic stem cells. Mol. Reprod. Dev. 56: 113-123.
27. Bassett, D. E., Jr., Eisen, M. B., and Boguski, M. S. (1999). Gene expression informatics - It's all in your mine. Nat. Genet. 21: 51-55.
28. Chen, Y., Dougherty, E. R., and Bittner, M. (1997). Ratio based decisions and the quantitative analysis of cDNA microarray images. J. Biomed. Opt. 2: 364-374.
29. Burn, T. C., Petrovick, M. S., Hohaus, S., Rollins, B. J., and Tenen, D. G. (1994). Monocyte chemoattractant protein-1 gene is expressed in activated neutrophils and retinoic acid-induced human myeloid cell lines. Blood 84: 2776-2783.
30. Jing, Y., et al. (2001). Combined effect of all-trans retinoic acid and arsenic trioxide in acute promyelocytic leukemia cells in vitro and in vivo. Blood 97: 264-269.
31. Horie, S., et al. (2001). Acceleration of thrombomodulin gene transcription by retinoic acid: Retinoic acid receptors and Sp1 regulate the promoter activity through interactions with two different sequences in the 5′-flanking region of human gene. J. Biol. Chem. 276: 2440-2450.
32. Platko, J. D., and Yen, A. (1997). Paxillin increases as retinoic acid or vitamin D3 induce HL-60 cell differentiation. In Vitro Cell Dev. Biol. Anim. 33: 84-87.
33. Benedetti, L., et al. (1996). Retinoid-induced differentiation of acute promyelocytic leukemia involves PML-RARα-mediated increase of type II transglutaminase. Blood 87: 1939-1950.
34. Takenaga, K., Nakamura, Y., and Sakiyama, S. (1994). Expression of a calcium binding protein pEL98 (mts1) during differentiation of human promyelocytic leukemia HL-60 cells. Biochem. Biophys. Res. Commun. 202: 94-101.
35. Katagiri, K., et al. (1996). Lyn and Fgr protein-tyrosine kinases prevent apoptosis during retinoic acid-induced granulocytic differentiation of HL-60 cells. J. Biol. Chem. 271: 11557-11562.
36. Rius, C., Vilaboa, N., Mata, F., and Aller, P. (1993). Differential modulation of the expression of the intermediate filament proteins vimentin and nuclear lamins A and C by differentiation inducers in human myeloid leukemia (U-937, HL-60) cells. Exp. Cell Res. 208: 115-120.
37. Delia, D., et al. (1995). Regulation of apoptosis induced by the retinoid N-(4-hydroxyphenyl) retinamide and effect of deregulated bcl-2. Blood 85: 359-367.
38. Kerr, M. K., and Churchill, G. A. (2001). Bootstrapping cluster analysis: Assessing the reliability of conclusions from microarray experiments. Proc. Natl. Acad. Sci. USA 98: 8961-8965.
39. Young, R. A. (2000). Biomedical discovery with DNA arrays. Cell 102: 9-15.
40. Hughes, T. R., et al. (2000). Functional discovery via a compendium of expression profiles. Cell 102: 109-126.
41. Mills, J. C., Roth, K. A., Cagan, R. L., and Gordon, J. I. (2001). DNA microarrays and beyond: Completing the journey from tissue to cell. Nat. Cell Biol. 3: E175-178.
42. D'Sa-Eipper, C., and Chinnadurai, G. (1998). Functional dissection of Bfl-1, a Bcl-2 homolog: Anti-apoptosis, oncogene-cooperation and cell proliferation activities. Oncogene 16: 3105-3114.
43. Sobek-Klocke, I., et al. (1997). The human gene ZFP161 on 18p11.21-pter encodes a putative c-myc repressor and is homologous to murine Zfp161 (Chr 17) and Zfp161-rs1 (X Chr). Genomics 43: 156-164.
44. Papoulis, A. (1991). Probability, Random Variables and Stochastic Processes. McGraw Hill, New York.
45. Bezdek, J. C. (1981). Pattern Recognition with Fuzzy Objective Function Algorithms. Plenum Press, New York.