@article{TEXTUAL,
      recid = {5803},
      author = {Veyrieras, Jean-Baptiste and Gaffney, Daniel J. and  Pickrell, Joseph K. and Gilad, Yoav and Stephens, Matthew  and Pritchard, Jonathan K.},
      title = {Exon-Specific QTLs Skew the Inferred Distribution of  Expression QTLs Detected Using Gene Expression Array Data},
      journal = {PLOS ONE},
      address = {2012-02-16},
      number = {TEXTUAL},
      abstract = {Mapping of expression quantitative trait loci (eQTLs) is  an important technique for studying how genetic variation  affects gene regulation in natural populations. In a  previous study using Illumina expression data from human  lymphoblastoid cell lines, we reported that cis-eQTLs are  especially enriched around transcription start sites (TSSs)  and immediately upstream of transcription end sites (TESs).  In this paper, we revisit the distribution of eQTLs using  additional data from Affymetrix exon arrays and from RNA  sequencing. We confirm that most eQTLs lie close to the  target genes; that transcribed regions are generally  enriched for eQTLs; that eQTLs are more abundant in exons  than introns; and that the peak density of eQTLs occurs at  the TSS. However, we find that the intriguing TES peak is  greatly reduced or absent in the Affymetrix and RNA-seq  data. Instead our data suggest that the TES peak observed  in the Illumina data is mainly due to exon-specific QTLs  that affect 3′ untranslated regions, where most of the  Illumina probes are positioned. Nonetheless, we do observe  an overall enrichment of eQTLs in exons versus introns in  all three data sets, consistent with an important role for  exonic sequences in gene regulation.},
      url = {http://knowledge.uchicago.edu/record/5803},
}