title: Identifying SNP targeted pathways in partial epilepsies with genome-wide association study data.
abstract: OBJECTIVE
  In a recent genome-wide association study for partial epilepsies in the European population, a common genetic variation has been reported to affect partial epilepsy only modestly. However, in complex diseases such as partial epilepsy, multiple factors (e.g. single nucleotide polymorphisms, microRNAs, metabolic and epigenetic factors) may target different sets of genes in the same pathway, affecting its function and thus causing the disease development. In this regard, we hypothesize that the pathways are critical for elucidating the mechanisms underlying partial epilepsy.
  
  
  METHODS
  Previously we had developed a novel methodology with the aim of identifying the disease-related pathways. We had combined evidence of genetic association with current knowledge of (i) biochemical pathways, (ii) protein-protein interaction networks, and (iii) the functional information of selected single nucleotide polymorphisms. In our present study, we apply this methodology to a data set on partial epilepsy, including 3445 cases and 6935 controls of European ancestry.
  
  
  RESULTS
  We have identified 30 overrepresented pathways with corrected p-values smaller than 10(-12). These pathways include complement and coagulation cascades, cell cycle, focal adhesion, extra cellular matrix-receptor interaction, JAK-STAT signaling pathway, MAPK signaling pathway, proteasome, ribosome, calcium signaling and regulation of actin cytoskeleton pathways. Most of these pathways have growing scientific support in the literature as being associated with partial epilepsy. We also demonstrate that different factors affect distinct parts of the pathways, as shown here on complement and coagulation cascades pathway with a comparison of gene expression vs. genome-wide association study.
  
  
  CONCLUSIONS
  Traditional studies on genome-wide association have not revealed strong associations in epilepsies, since these single nucleotide polymorphisms are not shared by most of the patients. Our results suggest that it is more effective to incorporate the functional effect of a single nucleotide polymorphism on the gene product, protein-protein interaction networks and functional enrichment tools into genome-wide association studies. These can then be used to determine leading molecular pathways, which cannot be detected through traditional analyses. We hope that this type of analysis brings the research community one step closer to unraveling the complex genetic structure of epilepsies.
authors.affiliation: Department of Genetics and Bioinformatics, Faculty of Arts and Sciences, Bahcesehir University, Ciragan Cad. Osmanpasa Mektebi Sok., No.: 4, 34353, Besiktas, Istanbul, Turkey. burcu.gungor@bahcesehir.edu.tr
authors.forename: B
authors.initials: B
authors.lastname: Bakir-Gungor
authors.forename: B
authors.initials: B
authors.lastname: Baykan
authors.forename: S
authors.initials: S
authors.lastname: Ugur İseri
authors.forename: F N
authors.initials: FN
authors.lastname: Tuncer
authors.forename: O U
authors.initials: OU
authors.lastname: Sezerman
mesh_terms: D030541:Databases, Genetic; D004828:Epilepsies, Partial / Q000175:diagnosis / Q000453:epidemiology / Q000235:genetics*; D053263:Gene Regulatory Networks / Q000235:genetics*; D055106:Genome-Wide Association Study / Q000379:methods*; D006801:Humans; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015398:Signal Transduction / Q000235:genetics*