DNA microarrays in parasitology: Strengths and limitations

Trends in Parasitology

Volumn 19, Issue 10, 2003, Pages 470-476

  Boothroyd, John C ^a   Blader, Ira ^a,b   Cleary, Michael ^a   Singh, Upinder ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF OKLAHOMA COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FLUORESCENT DYE; GENOMIC DNA;

AMPLICON; ANALYTIC METHOD; COMPARATIVE STUDY; DATA BASE; DNA LIBRARY; DNA MICROARRAY; DNA POLYMORPHISM; DNA PROBE; ENTAMOEBA DISPAR; ENTAMOEBA HISTOLYTICA; ESCHERICHIA COLI; EXPERIMENTAL DESIGN; FLAGELLATE; GENE AMPLIFICATION; GENE CONTROL; GENE EXPRESSION; GENE SEQUENCE; GENETIC ANALYSIS; GENOME; GENOMICS; GENOTYPE; HOST PARASITE INTERACTION; HUMAN; IMMUNE RESPONSE; INFORMATION PROCESSING; LEISHMANIA; LIFE CYCLE; METHODOLOGY; MYCOBACTERIUM BOVIS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PARASITE DEVELOPMENT; PLASMODIUM FALCIPARUM; PLASMODIUM VIVAX; POLYMERASE CHAIN REACTION; PUBLICATION; REPRODUCIBILITY; REVIEW; RNA TRANSLATION; SAMPLE; STATISTICAL ANALYSIS; THEILERIA PARVA; TOXOPLASMA GONDII; TRYPANOSOMA CRUZI; VIBRIO CHOLERAE;

ANIMALS; CHROMOSOME MAPPING; GENE EXPRESSION REGULATION; HUMANS; MOLECULAR PROBE TECHNIQUES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PARASITES; REPRODUCIBILITY OF RESULTS;

ENTAMOEBA; ENTAMOEBA DISPAR; ENTAMOEBA HISTOLYTICA; ESCHERICHIA COLI; MASTIGOPHORA (FLAGELLATES); MYCOBACTERIUM; MYCOBACTERIUM BOVIS; MYCOBACTERIUM TUBERCULOSIS; PLASMODIUM FALCIPARUM; PLASMODIUM VIVAX; THEILERIA; THEILERIA PARVA; TOXOPLASMA GONDII; TRYPANOSOMA; TRYPANOSOMA CRUZI; VIBRIO; VIBRIO CHOLERAE;

EID: 0842292814     PISSN: 14714922     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pt.2003.08.002     Document Type: Review

References (44)

1. Rathod P.K., et al. DNA microarrays for malaria. Trends Parasitol. 18:2002;39-45.
2. Duggan D.J., et al. Expression profiling using cDNA microarrays. Making and reading microarrays. Nat. Genet. 1:(Suppl):1999;10-14.
3. Le Roch K.G., et al. Monitoring the chromosome 2 intraerythrocytic transcriptome of Plasmodium falciparum using oligonucleotide arrays. Am. J. Trop. Med. Hyg. 67:2002;233-243.
4. Volkman S.K., et al. Excess polymorphisms in genes for membrane proteins in Plasmodium falciparum. Science. 298:2002;216-218.
5. Lockhart D.J., et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 14:1996;1675-1680.
6. Miller L.D., et al. Optimal gene expression analysis by microarrays. Cancer Cell. 2:2002;353-361.
7. Eisen M.B., Brown P.O. DNA arrays for analysis of gene expression. Methods Enzymol. 303:1999;179-205.
8. Richter A., et al. Comparison of fluorescent tag DNA labeling methods used for expression analysis by DNA microarrays. Biotechniques. 33:2002;620-630.
9. Alizadeh A.A., et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 403:2000;503-511.
10. Cleary M.D., et al. Toxoplasma gondii asexual development: identification of developmentally regulated genes and distinct patterns of gene expression. Eukaryot. Cell. 1:2002;329-340.
11. Dudley A.M., et al. Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc. Natl. Acad. Sci. U. S. A. 99:2002;7554-7559.
12. Sterrenburg E., et al. A common reference for cDNA microarray hybridizations. Nucleic Acids Res. 30:2002;E116.
13. Knight J. When the chips are down. Nature. 410:2001;860-861.
14. Tusher V.G., et al. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. U. S. A. 98:2001;5116-5121.
15. Mills J.C., et al. DNA microarrays and beyond: completing the journey from tissue to cell. Nat. Cell Biol. 3:2001;E175-E178.
16. Stears R.L., et al. A novel, sensitive detection system for high-density microarrays using dendrimer technology. Physiol. Genomics. 3:2000;93-99.
17. Karsten S.L., et al. An evaluation of tyramide signal amplification and archived fixed and frozen tissue in microarray gene expression analysis. Nucleic Acids Res. 30:2002;E4.
18. Manduchi E., et al. Comparison of different labeling methods for two-channel high-density microarray experiments. Physiol. Genomics. 10:2002;169-179.
19. Luo L., et al. Gene expression profiles of laser-captured adjacent neuronal subtypes. Nat. Med. 5:1999;117-122.
20. Gelder R., et al. Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc. Natl. Acad. Sci. U. S. A. 87:1990;1663-1667.
21. Diamond L.S., Clark C.G. A redescription of Entamoeba-histolytica schaudinn, 1903 (emended Walker; 1911) separating it from Entamoeba dispar Brumpt, 1925. J. Eukaryot. Microbiol. 40:1993;340-344.
22. Clark C.G., Diamond L.S. Intraspecific variation and phylogenetic relationships in the genus Entamoeba as revealed by riboprinting. J. Eukaryot. Microbiol. 44:1997;142-154.
23. Merrell D.S., et al. Host-induced epidemic spread of the cholera bacterium. Nature. 417:2002;642-645.
24. Behr M.A., et al. Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science. 284:1999;1520-1523.
25. Masuda N., Church G.M. Escherichia coli gene expression responsive to levels of the response regulator EvgA. J. Bacteriol. 184:2002;6225-6234.
26. Dunman P.M., et al. Transcription profiling-based identification of Staphylococcus aureus genes regulated by the agr and/or sarA loci. J. Bacteriol. 183:2001;7341-7353.
27. Singh U., et al. Genetic analysis of tachyzoite to bradyzoite differentiation mutants in Toxoplasma gondii reveals a hierarchy of gene induction. Mol. Microbiol. 44:2002;721-733.
28. Mamoun C.B., et al. Co-ordinated programme of gene expression during asexual intraerythrocytic development of the human malaria parasite Plasmodium falciparum revealed by microarray analysis. Mol. Microbiol. 39:2001;26-36.
29. Manger I.D., et al. Expressed sequence tag analysis of the bradyzoite stage of Toxoplasma gondii: identification of developmentally regulated genes. Infect. Immun. 66:1998;1632-1637.
30. Clayton C.E. Life without transcriptional control? From fly to man and back again. EMBO J. 21:2002;1881-1888.
31. Gingras A.-C., et al. eIF4 initiation factors: effectors of mRNA recruitment to ribosomes and regulators of translation. Annu. Rev. Biochem. 68:1999;913-963.
32. Kraggerud S.M., et al. Regulation of protein-synthesis in human cells exposed to extreme hypoxia. Anticancer Res. 15:1995;683-686.
33. Zong Q., et al. Messenger RNA translation state: the second dimension of high-throughput expression screening. Proc. Natl. Acad. Sci. U. S. A. 96:1999;10632-10636.
34. Kuhn K.M., et al. Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source. Mol. Cell. Biol. 21:2001;916-927.
35. Diehn M., et al. Large-scale identification of secreted and membrane-associated gene products using DNA microarrays. Nat. Genet. 25:2000;58-62.
36. Blader I.J., et al. Microarray analysis reveals previously unknown changes in Toxoplasma gondii-infected human cells. J. Biol. Chem. 276:2001;24223-24231.
37. Huang Q., et al. The plasticity of dendritic cell responses to pathogens and their components. Science. 294:2001;870-875.
38. Boldrick J.C., et al. Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Proc. Natl. Acad. Sci. U. S. A. 99:2002;972-977.
39. de Avalos S.V., et al. Immediate/early response to Trypanosoma cruzi infection involves minimal modulation of host cell transcription. J. Biol. Chem. 277:2001;639-644.
40. Guillemin K., et al. Cag pathogenicity island-specific responses of gastric epithelial cells to Helicobacter pylori infection. Proc. Natl. Acad. Sci. U. S. A. 99:2002;15136-15141.
41. Geiss G.K., et al. Large-scale monitoring of host cell gene expression during HIV-1 infection using cDNA microarrays. Virology. 266:2000;8-16.
42. Chang Y., Laimins L. Microarray analysis identifies interferon-inducible genes and Stat1 as major transcriptional targets of human papillomavirus type 31. J. Virol. 74:2000;4174-4182.
43. Cohen P., et al. Monitoring cellular responses to Listeria monocytogenes with oligonucleotide arrays. J. Biol. Chem. 275:2000;11181-11190.
44. Renne R., et al. Modulation of cellular and viral gene expression by the latency-associated nuclear antigen of Kaposi's sarcoma-associated herpesvirus. J. Virol. 75:2001;458-468.