Application of Gene Network Analysis Techniques Identifies AXIN1/PDIA2 and Endoglin Haplotypes Associated with Bicuspid Aortic Valve (original) (raw)
Figure 1
Schematic Representation of SNP Prioritization.
The 311,399 SNPs present on the Illumina CNV370 (representing about 15,000 well annotated genes) are prioritized by three methods. The “knowledge-based” approach involves expression analysis and inclusion of existing annotations, term extension by CANDID or STRING network-based analysis, and ultimately leading to the output of a gene list. Probes inside and within regulatory regions of these genes are then selected for association analysis. Probe results for the STRING arm are shown as an example: 8,801 SNPs representing approximately 815 prioritized genes. In parallel, SNPs are prioritized by Random Forest analysis, which recursively partitions the data to reveal SNPs with highest likelihood of successful association results. Finally, fitSNPs (derived independently of this study) represented on the CNV370 array are analyzed for association.