Exon-based mapping of microarray probes: recovering differential gene expression signal in underpowered hypoxia experiment.

ABSTRACT: There is an immense collection of underpowered Affymetrix gene array experiments. Although a majority of these experiments generated biologically feasible results, the considerable fraction of assays failed to identify expected transcriptional changes. There is an unused potential of Affymetrix probe-set redundancy for common exonic and UTR regions. We hypothesized that group analysis of multiple probe-sets which hybridize to the same exon or UTR will increase array discriminating power of transcriptional changes. To test this hypothesis, we analyzed Affymetrix mouse probe-sets that share the same exon using blocking feature of the Significance Analysis of Microarrays (SAM). Two-thousand two-hundred one exon-sharing probe-sets targeting 1011 transcripts were identified by mapping 36701 MG-

SUBMITTER: Grigoryev DN 

PROVIDER: S-EPMC1852466 | biostudies-literature | 2007 Apr

REPOSITORIES: biostudies-literature