25 research outputs found

    A list of five toxic chemicals discovered based on CTD as potentially toxic chemicals for UF.

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    A list of five toxic chemicals discovered based on CTD as potentially toxic chemicals for UF.</p

    Functional annotation networks consisting of biological pathways enriched with TWAS genes for UF.

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    (A) Four major clusters grouped into three parental biological pathways were enriched with positively associated TWAS genes (TWAS P-value 0). (B) Four major clusters of biological pathways were enriched with negatively associated TWAS genes (TWAS P-value < 0.05 and Z-score < 0). The major clusters are the sub-networks in the top 25% for connectivity score as calculated by the MCODE in each functional annotation network. Each node represented by a pie chart indicates an enriched biological pathway, and the sector size is proportional to the number of genes that originate from each tissue panel. The node size corresponds to the number of panels where TWAS genes were enriched.</p

    Manhattan plots of the UF GWAS summary statistics data analyzed and visualized by FUMA.

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    (A) A Manhattan plot of the input GWAS summary statistics. (B) A Manhattan plot of the MAGMA results. Significant prioritized genes associated with SNPs are visualized with gene symbols. The dashed red line indicates a Bonferroni significant threshold (P −6). (TIF)</p

    A ternary plot of colocalization test results.

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    PP0–4 indicate PPs of five hypotheses (H0–4). The gray dots are the genes that were not significant in either TWAS or the colocalization tests. The red and blue dots indicate the significantly associated genes in TWAS and the colocalization tests, respectively. The genes that were prioritized in both TWAS and the colocalization tests are represented as purple dots. (TIFF)</p

    Circos plots showing how marginally significant TWAS gene lists (P < 0.05) for each of the eight eQTL panels overlap.

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    On the outside, the arc represents the eight eQTL panels. On the inside, the dark orange arc represents genes shared by several panels and the light orange arc represents genes unique to those panels. The purple lines link the genes shared by several panels. (A) The plot shows the shared genes between positively associated TWAS genes (TWAS Z-score > 0). (B) The plot shows shared genes between negatively associated TWAS genes (TWAS Z-score (TIF)</p