Journal: PLoS ONE

Article Title: Application of Gene Network Analysis Techniques Identifies AXIN1/PDIA2 and Endoglin Haplotypes Associated with Bicuspid Aortic Valve

doi: 10.1371/journal.pone.0008830

Figure Lengend Snippet: 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.

Article Snippet: Separately, we identified the 8,801 Functionally Interpolating SNPs (fitSNPs) present on the Illumina 370CNV array.

Techniques: Expressing, Derivative Assay

Journal: PLoS ONE

Article Title: Application of Gene Network Analysis Techniques Identifies AXIN1/PDIA2 and Endoglin Haplotypes Associated with Bicuspid Aortic Valve

doi: 10.1371/journal.pone.0008830

Figure Lengend Snippet: Prioritized Probe distribution by category.

Article Snippet: Separately, we identified the 8,801 Functionally Interpolating SNPs (fitSNPs) present on the Illumina 370CNV array.

Techniques:

Journal: PLoS ONE

Article Title: Application of Gene Network Analysis Techniques Identifies AXIN1/PDIA2 and Endoglin Haplotypes Associated with Bicuspid Aortic Valve

doi: 10.1371/journal.pone.0008830

Figure Lengend Snippet: ab initio Probe distribution by category: Categories in italics represent shared probes from those respective classes.

Article Snippet: Separately, we identified the 8,801 Functionally Interpolating SNPs (fitSNPs) present on the Illumina 370CNV array.

Techniques:

Journal: PLoS ONE

Article Title: Application of Gene Network Analysis Techniques Identifies AXIN1/PDIA2 and Endoglin Haplotypes Associated with Bicuspid Aortic Valve

doi: 10.1371/journal.pone.0008830

Figure Lengend Snippet: Data from three approaches and relevant genomic features extracted from the Ensembl 54 database are depicted. At the top of the plot is an ideogram depicting a location on chromosome 16; the small red box delimits a region between base pair 212416 and 407490, displayed immediately below the ideogram (track labeled “bp” which also indicates the 5′ to 3′ orientation of the plot). Annotated gene content is displayed on positive (denoted by “+”) and negative (denoted by “−”) strand. The four graphical data-panes indicate RR cM/Mb: relative recombination rate in centimorgans per megabase as derived from HapMap build 36. STRING −log(p), CANDID −log(p), and fitSNPs −log(p): −log 10 uncorrected p-values observed in each of the three indicated schemes. All probes analyzed in the region by each respective schema are represented by a peak. The region between the two tallest peaks in the STRING and CANDID plots delineates the observed haplotype detailed in .

Article Snippet: Separately, we identified the 8,801 Functionally Interpolating SNPs (fitSNPs) present on the Illumina 370CNV array.

Techniques: Labeling, Derivative Assay