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

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-U74v2 probe-sets to genomic alignments of 3,971,086 known mouse transcripts. Using the blocking feature of SAM with an underpowered (two microarrays per experimental condition) mouse hypoxia-induced pulmonary hypertension model, we identified 24 genes that were significantly (FDR<5%) affected by hypoxia but were not detected by regular SAM. The relevance of the four newly identified genes (Mig6, F3, Bmp6, and Ndrg1) to known hypoxia-associated responses was confirmed by PubMatrix; and hypoxia-induced up-regulation of Mig6 expression was validated by real-time RT-PCR. We demonstrated that analysis of exon-sharing probe-sets allowed discovery of additional hypoxia-affected genes in an underpowered array experiment. This method will facilitate re-evaluation of existing underpowered Affymetrix gene expression profiles.