Using DNA microarrays to study gene expression in closely related species
- Author(s)
- Oshlack, A; Chabot, AE; Smyth, GK; Gilad, Y;
- Details
- Publication Year 2007-05-15,Volume 23,Issue #10,Page 1235-1242
- Journal Title
- BIOINFORMATICS
- Publication Type
- Journal Article
- Abstract
- Motivation: Comparisons of gene expression levels within and between species have become a central tool in the study of the genetic basis for phenotypic variation, as well as in the study of the evolution of gene regulation. DNA microarrays are a key technology that enables these studies. Currently, however, microarrays are only available for a small number of species. Thus, in order to study gene expression levels in species for which microarrays are not available, researchers face three sets of choices: (i) use a microarray designed for another species, but only compare gene expression levels within species, (ii) construct a new microarray for every species whose gene expression profiles will be compared or (iii) build a multispecies microarray with probes from each species of interest. Here, we use data collected using a multi-primate cDNA array to evaluate the reliability of each approach. Results: We find that, for inter-species comparisons, estimates of expression differences based on multi-species microarrays are more accurate than those based on multiple species-specific arrays. We also demonstrate that within-species expression differences can be estimated using a microarray for a closely related species, without discernible loss of information.
- Publisher
- OXFORD UNIV PRESS
- Keywords
- C VIRUS-INFECTION; SEQUENCE DIVERGENCE; EVOLUTION; PATTERNS; CHIMPANZEES; DROSOPHILA; PRIMATES; REPRODUCIBILITY; NORMALIZATION; PROFILES
- Publisher's Version
- https://doi.org/10.1093/bioinformatics/btm111
- Terms of Use/Rights Notice
- Refer to copyright notice on published article.
Creation Date: 2007-05-15 12:00:00