Analysis of result variability from high-density oligonucleotide arrays comparing same-species and cross-species hybridizations

BioTechniques

Volumn 33, Issue 3, 2002, Pages 516-524

  Chismar, J D ^a   Mondala, T ^a   Fox, H S ^a   Roberts, E ^a   Langford, D ^a   Masliah, E ^a   Salomon, D R ^a   Head, S R ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARRAYS; BIODIVERSITY; GENETIC ENGINEERING; RNA;

HYBRIDIZATIONS;

BIOTECHNOLOGY;

OLIGONUCLEOTIDE; RNA;

ARTICLE; CONTROLLED STUDY; DNA MICROARRAY; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GENOME; HUMAN; HYBRIDIZATION; NONHUMAN; QUALITY CONTROL; RHESUS MONKEY; RNA ANALYSIS; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; TECHNIQUE; ANALYSIS OF VARIANCE; ANIMAL; COMPARATIVE STUDY; DNA PROBE; EVALUATION; GENETIC VARIABILITY; GENETICS; INSTRUMENTATION; MACACA; METHODOLOGY; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY;

MACACA MULATTA; PRIMATES;

ANALYSIS OF VARIANCE; ANIMALS; DNA PROBES; HUMANS; HYBRIDIZATION, GENETIC; MACACA MULATTA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS; RNA; SENSITIVITY AND SPECIFICITY; SPECIES SPECIFICITY; VARIATION (GENETICS);

EID: 0036752861     PISSN: 07366205     EISSN: None     Source Type: Journal    
DOI: 10.2144/02333st01_11836a     Document Type: Article

References (13)

1. Bigger, C.B., K.M. Brasky, and R.E. Lanford. 2001. DNA microarray analysis of chimpanzee liver during acute resolving hepatitis C virus infection. J. Virol. 75:7059-7066.
2. Cavallaro, S., B.G. Schreurs, W. Zhao, V. D'Agata, and D.L. Alkon. 2001. Gene expression profiles during long-term memory consolidation. Eur. J. Neurosci. 9:1809-1815.
3. Enard, W., P. Khaitovich, J. Klose, S. Zollner, F. Heissig, P. Giavalisco, K. Nieselt-Struwe, E. Muchmore, et al. 2002. Intra- and interspecific variation in primate gene expression patterns. Science 5566:340-343.
4. Frazer, K.A., J.B. Sheehan, R.P. Stokowski, X. Chen, R. Hosseini, J.F. Cheng, S.P. Fodor, D.R. Cox, and N. Patil. 2001. Evolutionarily conserved sequences on human chromosome 21. Genome Res. 11:1651-1659.
5. Hacia, J.G., J.B. Fan, O. Ryder, L. Jin, K. Edgemon, G. Ghandour, R.A. Mayer, B. Sun, et al. 1999. Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays. Nat. Genet. 2:164-167.
6. Hacia, J.G., W. Makalowski, K. Edgemon, M.R. Erdos, C.M. Robbins, S.P. Fodor, L.C. Brody, and F.S. Collins. 1998. Evolutionary sequence comparisons using high-density oligonucleotide arrays. Nat. Genet. 18:155-158.
7. Kayo, T. D.B. Allison, R. Weindruch, T.A. Prolla. 2001. Influences of aging and caloric restriction on the transcriptional profile of skeletal muscle from rhesus monkeys. Proc. Natl. Acad. Sci. USA 9:5093-5098.
8. Li, C. and W.H. Wong. 2001. Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. Proc. Natl. Acad. Sci. USA 98:31-36.
9. Lipshutz, R.J., S.P. Fodor, T.R. Gingeras, and D.J. Lockhart. 1999. High density synthetic oligonucleotide arrays. Nat. Genet. 21:20-24.
10. Lockhart, D.J., H. Dong, M.C. Byrne, M.T. Follettie, M.V. Gallo, M.S. Chee, M. Mittmann, C. Wang, et al. 1996. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 13:1675-1680.
11. Nau, M.E., R.E. Lyndal, R.K. Martin, D.E. Kyle, D.F. Wirth, and M. Vahey. 2000. Technical assessment of the Affymetrix yeast expression GeneChip YE6 100 platform in a heterologous model of genes that confer resistance to antimalarial drugs in yeast. J. Clin. Microbiol. 5:1901-1908.
12. Mills, J.C. and J.I. Gordon. 2001. A new approach for filtering noise from high-density oligonucleotide microarray datasets. Nucleic Acids Res. 15:E72-2.
13. Schadt, E.E., C. Li, C. Su, and W.H. Wong. 2000. Analyzing high-density oligonucleotide gene expression array data. J. Cell Biochem. 80:192-202.