title: Jetset: selecting the optimal microarray probe set to represent a gene.
abstract: 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.
authors.affiliation: Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark.
authors.forename: Qiyuan
authors.initials: Q
authors.lastname: Li
authors.forename: Nicolai J
authors.initials: NJ
authors.lastname: Birkbak
authors.forename: Balazs
authors.initials: B
authors.lastname: Gyorffy
authors.forename: Zoltan
authors.initials: Z
authors.lastname: Szallasi
authors.forename: Aron C
authors.initials: AC
authors.lastname: Eklund
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics; D005091:Exons; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D018719:Erb-b2 Receptor Tyrosine Kinases / Q000235:genetics; D011960:Receptors, Estrogen / Q000235:genetics; D012680:Sensitivity and Specificity
chemical_list: D018719:Erb-b2 Receptor Tyrosine Kinases; D011960:Receptors, Estrogen; C508053:ERBB2 protein, human