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

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

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

Dmitry N Grigoryev,Shwu-Fan Ma,Larissa A Shimoda,Roger A Johns,Byungkook Lee,Joe G N Garcia,

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.

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

DN Grigoryev,SF Ma,LA Shimoda,RA Johns,B Lee,JG Garcia,

For similar investigative techniques: genetic techniques: sequence alignment research abstracts see: investigative techniques: genetic techniques: sequence alignment research

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

PUBLICATION TYPE: Research Support, N.I.H., Extr

Journal: Molecular and cellular probes

VOLUME: 21

Page Numbers: 134-9

Journal Abbreviation: Mol. Cell. Probes

ISSN: 0890-8508

DAY: 19

MONTH: 09

YEAR: 2006

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

Number of References:

LANGUAGE: eng

NlmUniqueID: 8709751

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

KEYWORDS: Sequence Alignment

MESH TERMS: methods

Chemical & Substance for Abstract: Exon-based mapping of microarray probes: recovering differential gene expression signal in underpowered hypoxia experiment. Information

Substance Name: DNA Probes

Registry Number: 0

Grant and Affiliation Information for Exon-based mapping of microarray probes: recovering differential gene expression signal in underpowered hypoxia experiment.

AFFILIATION: Johns Hopkins University, School of Medicine, Baltimore, MD, USA. dgrigor1@jhmi.edu

Country: England

AGENCY: United States NHLBI

GRANT: HL-69340

ACRONYM: HL

MEDLINETA: Mol Cell Probes

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