Jetset: selecting the optimal microarray probe set to represent a gene

Qiyuan Li, Nicolai Juul Birkbak, Balazs Gyorffy, Zoltan Imre Szallasi, Aron Charles Eklund

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    Background: Interpretation of gene expression microarrays requires a mapping from probe set to gene. On many Affymetrix gene expression microarrays, a given gene may be detected by multiple probe sets, which may deliver inconsistent or even contradictory measurements. Therefore, obtaining an unambiguous expression estimate of a pre-specified gene can be a nontrivial but essential task. Results: We developed scoring methods to assess each probe set for specificity, splice isoform coverage, and robustness against transcript degradation. We used these scores to select a single representative probe set for each gene, thus creating a simple one-to-one mapping between gene and probe set. To test this method, we evaluated concordance between protein measurements and gene expression values, and between sets of genes whose expression is known to be correlated. For both test cases, we identified genes that were nominally detected by multiple probe sets, and we found that the probe set chosen by our method showed stronger concordance. Conclusions: This method provides a simple, unambiguous mapping to allow assessment of the expression levels of specific genes of interest.
    Original languageEnglish
    JournalB M C Bioinformatics
    Issue number1
    Pages (from-to)474
    Publication statusPublished - 2011

    Bibliographical note

    2011 Li et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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