PUBLICATION
Statistical evaluation of differential expression on cDNA nylon arrays with replicated experiments
- Authors
- Herwig, R., Aanstad, P., Clark, M., and Lehrach, H.
- ID
- ZDB-PUB-011203-3
- 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.
Citation
Herwig, R., Aanstad, P., Clark, M., and Lehrach, H. (2001) Statistical evaluation of differential expression on cDNA nylon arrays with replicated experiments. Nucleic acids research. 29(23):U1-U9.
Abstract
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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping