Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays.

ABSTRACT:

Background

Alternative mRNA processing mechanisms lead to multiple transcripts (i.e. splice isoforms) of a given gene which may have distinct biological functions. Microarrays like Affymetrix GeneChips measure mRNA expression of genes using sets of nucleotide probes. Until recently probe sets were not designed for transcript specificity. Nevertheless, the re-analysis of established microarray data using newly defined transcript-specific probe sets may provide information about expression levels of specific transcripts.

Methodology/principal findings

In the present study alignment of probe sequences of the Affymetrix microarray HG-U133A with Ensembl transcript sequences was performed to define transcript-specific probe sets. Out of a total of 247,965 perfect match probes, 95,

SUBMITTER: Moll AG 

PROVIDER: S-EPMC2650090 | biostudies-literature | 2009

REPOSITORIES: biostudies-literature