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Cross-platform prediction of gene expression signatures.

Publication ,  Journal Article
Lin, S-H; Beane, L; Chasse, D; Zhu, KW; Mathey-Prevot, B; Chang, JT
Published in: PLoS One
2013

Gene expression signatures can predict the activation of oncogenic pathways and other phenotypes of interest via quantitative models that combine the expression levels of multiple genes. However, as the number of platforms to measure genome-wide gene expression proliferates, there is an increasing need to develop models that can be ported across diverse platforms. Because of the range of technologies that measure gene expression, the resulting signal values can vary greatly. To understand how this variation can affect the prediction of gene expression signatures, we have investigated the ability of gene expression signatures to predict pathway activation across Affymetrix and Illumina microarrays. We hybridized the same RNA samples to both platforms and compared the resultant gene expression readings, as well as the signature predictions. Using a new approach to map probes across platforms, we found that the genes in the signatures from the two platforms were highly similar, and that the predictions they generated were also strongly correlated. This demonstrates that our method can map probes from Affymetrix and Illumina microarrays, and that this mapping can be used to predict gene expression signatures across platforms.

Duke Scholars

Published In

PLoS One

DOI

EISSN

1932-6203

Publication Date

2013

Volume

8

Issue

11

Start / End Page

e79228

Location

United States

Related Subject Headings

  • Oligonucleotide Array Sequence Analysis
  • Humans
  • Genome-Wide Association Study
  • General Science & Technology
  • Gene Expression Regulation
  • Gene Expression Profiling
  • Cell Line, Tumor
 

Citation

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MLA
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Lin, S.-H., Beane, L., Chasse, D., Zhu, K. W., Mathey-Prevot, B., & Chang, J. T. (2013). Cross-platform prediction of gene expression signatures. PLoS One, 8(11), e79228. https://doi.org/10.1371/journal.pone.0079228
Lin, Shu-Hong, Lauren Beane, Dawn Chasse, Kevin W. Zhu, Bernard Mathey-Prevot, and Jeffrey T. Chang. “Cross-platform prediction of gene expression signatures.PLoS One 8, no. 11 (2013): e79228. https://doi.org/10.1371/journal.pone.0079228.
Lin S-H, Beane L, Chasse D, Zhu KW, Mathey-Prevot B, Chang JT. Cross-platform prediction of gene expression signatures. PLoS One. 2013;8(11):e79228.
Lin, Shu-Hong, et al. “Cross-platform prediction of gene expression signatures.PLoS One, vol. 8, no. 11, 2013, p. e79228. Pubmed, doi:10.1371/journal.pone.0079228.
Lin S-H, Beane L, Chasse D, Zhu KW, Mathey-Prevot B, Chang JT. Cross-platform prediction of gene expression signatures. PLoS One. 2013;8(11):e79228.

Published In

PLoS One

DOI

EISSN

1932-6203

Publication Date

2013

Volume

8

Issue

11

Start / End Page

e79228

Location

United States

Related Subject Headings

  • Oligonucleotide Array Sequence Analysis
  • Humans
  • Genome-Wide Association Study
  • General Science & Technology
  • Gene Expression Regulation
  • Gene Expression Profiling
  • Cell Line, Tumor