ZFIN ID: ZDB-PUB-011203-3
Statistical evaluation of differential expression on cDNA nylon arrays with replicated experiments
Herwig, R., Aanstad, P., Clark, M., and Lehrach, H.
Date: 2001
Source: Nucleic acids research   29(23): U1-U9 (Review)
Registered Authors: Aanstad, Pia, Clark, Matthew D., Lehrach, Hans
Keywords: gene expression, oligonucleotide arrays, lithium, patterns, hybridization, sensitivity, zebrafish, libraries, pathway, embryo
MeSH Terms:
  • Animals
  • Arabidopsis/genetics
  • False Positive Reactions
  • Gene Expression Profiling/methods*
  • Gene Expression Profiling/statistics & numerical data*
  • In Situ Hybridization
  • Nylons/chemistry*
  • Oligonucleotide Array Sequence Analysis/methods*
  • Oligonucleotide Array Sequence Analysis/statistics & numerical data*
  • RNA, Messenger/biosynthesis
  • RNA, Plant/biosynthesis
  • Reproducibility of Results
  • Sample Size
  • Sensitivity and Specificity
  • Zebrafish/embryology
  • Zebrafish/genetics
  • Zebrafish/metabolism
PubMed: 11726700 Full text @ Nucleic Acids Res.
In this paper we focus on the detection of differentially expressed genes according to changes in hybridization signals using statistical tests. These tests were applied to 14 208 zebrafish cDNA clones that were immobilized on a nylon support and hybridized with radioactively labeled target mRNA from wild-type and lithium-treated zebrafish embryos. The methods were evaluated with respect to 16 control clones that correspond to eight different genes which are known to be involved in dorso-ventral axis specification. Moreover, 4608 Arabidopsis thaliana clones on the same array were used to judge statistical significance of expression changes and to control the false positive rates of the test decisions. Utilizing this special array design we show that differential expression of a high proportion of cDNA clones (15/16) and the respective genes (7/8) were identified, with a false positive error of <5% using the constant control data. Furthermore, we investigated the influence of the number of repetitions of experiments on the accuracy of the procedures with experimental and simulated data. Our results suggest that the detection of differential expression with repeated hybridization experiments is an accurate and sensitive way of identifying even small expression changes (1:1.5) of a large number of genes in parallel.