Single-species microarrays and comparative transcriptomics.

ABSTRACT:

Background

Prefabricated expression microarrays are currently available for only a few species but methods have been proposed to extend their application to comparisons between divergent genomes.

Methodology/principal findings

Here we demonstrate that the hybridization intensity of genomic DNA is a poor basis on which to select unbiased probes on Affymetrix expression arrays for studies of comparative transcriptomics, and that doing so produces spurious results. We used the Affymetrix Xenopus laevis microarray to evaluate expression divergence between X. laevis, X. borealis, and their F1 hybrids. When data are analyzed with probes that interrogate only sequences with confirmed identity in both species, we recover results that differ substantially analyses that use genomic DN

SUBMITTER: Chain FJ 

PROVIDER: S-EPMC2533705 | biostudies-literature | 2008 Sep

REPOSITORIES: biostudies-literature