title: An eQTL analysis of the human glioblastoma multiforme genome.
abstract: In this paper we use eQTL mapping to identify associations between gene dysregulation and single nucleotide polymorphism (SNP) genotypes in glioblastoma multiforme (GBM). A set of 532,954 SNPs was evaluated as predictors of the expression levels of 22,279 expression probes. We identified SNPs associated with fold change in expression level rather than raw expression levels in the tumor. Following adjustment for false discovery rate, the complete set of probes yielded 9257 significant associations (p<0.05). We found 18 eQTLs that were missense mutations. Many of the eQTLs in the non-coding regions of a gene, or linked to nearby genes, had large numbers of significant associations (e.g. 321 for RNASE3, 101 for BNC2). Functional enrichment analysis revealed that the expression probes in significant associations were involved in signal transduction, transcription regulation, membrane function, and cell cycle regulation. These results suggest several loci that may serve as hubs in gene regulatory pathways associated with GBM.
authors.affiliation: NeuroTexas Institute, St. David's Healthcare, Austin, TX 78705, USA; Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA; Fresh Pond Research Institute, Cambridge MA 02140, USA. Electronic address: shpak.max@gmail.com.
authors.forename: Max
authors.initials: M
authors.lastname: Shpak
authors.affiliation: Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA.
authors.forename: Amelia Weber
authors.initials: AW
authors.lastname: Hall
authors.affiliation: Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA.
authors.forename: Marcus M
authors.initials: MM
authors.lastname: Goldberg
authors.affiliation: Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA.
authors.forename: Dakota Z
authors.initials: DZ
authors.lastname: Derryberry
authors.affiliation: Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA.
authors.forename: Yunyun
authors.initials: Y
authors.lastname: Ni
authors.affiliation: Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA; Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA.
authors.forename: Vishwanath R
authors.initials: VR
authors.lastname: Iyer
authors.affiliation: Texas Advanced Computing Center, University of Texas, Austin, TX 78758, USA.
authors.forename: Matthew C
authors.initials: MC
authors.lastname: Cowperthwaite
mesh_terms: D001932:Brain Neoplasms / Q000235:genetics*; D015972:Gene Expression Regulation, Neoplastic; D015894:Genome, Human; D005909:Glioblastoma / Q000235:genetics*; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci
keywords: Gene expression; Glioblastoma multiforme; eQTL