TY - JOUR
T1 - Exon-based mapping of microarray probes
T2 - Recovering differential gene expression signal in underpowered hypoxia experiment
AU - Grigoryev, Dmitry N.
AU - Ma, Shwu Fan
AU - Shimoda, Larissa A.
AU - Johns, Roger A.
AU - Lee, Byungkook
AU - Garcia, Joe G.N.
N1 - Funding Information:
We thank Eric Hoffman for generating, organizing and publishing pertinent to this manuscript array data on his PEPR website ( http://pepr.cnmcresearch.org ), and Karen Maresso for helpful suggestions on the manuscript compilation. This work was supported by the NHLBI—sponsored HopGene Program in Genomics Application (HL-69340) and individual (DNG) NRSA grant (F32 HL74590-01A1).
PY - 2007/4
Y1 - 2007/4
N2 - 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.
AB - 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.
KW - Gene expression profiling
KW - Hypoxia
KW - Microarray
KW - Mouse model
KW - Oligonucleotide probe
KW - Pulmonary hypertension
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U2 - 10.1016/j.mcp.2006.09.002
DO - 10.1016/j.mcp.2006.09.002
M3 - Article
C2 - 17071053
AN - SCOPUS:33846060162
SN - 0890-8508
VL - 21
SP - 134
EP - 139
JO - Molecular and Cellular Probes
JF - Molecular and Cellular Probes
IS - 2
ER -