Analysis strategy for the identification of miRNA-mediated <i>cis</i>-eQTL effects.

<p>(a) <i>Cis</i>-eQTL SNPs and their perfect proxies (R² = 1, 1000G CEU population) were mapped to the 3' UTRs of <i>cis</i>-affected ENSEMBL transcripts. Next, the SNPs that were located within the <i>in silico</i> miRNA binding sites were identified from public databases PolymiRTS, miRSNP, and webtool mrSNP, each utilizing a different <i>in silico</i> target prediction algorithm. The direction of allelic trends was assessed for concordance with the logic of miRNA-mediated regulation. (b) Associations between Illumina expression probes, MRE-SNPs, and miRNAs. An MRE-SNP-probe association consists of an MRE-SNP and an Illumina probe, detecting the corresponding <i>cis</i>-affected gene. An miR-SNP-probe association adds the miRNA, for which the predicted MRE is either disrupted or created by the MRE-SNP.</p

Top 30 filtered SNP-miR-probe associations, sorted based on their context+ scores.

<p>SNPs shown in bold are in experimentally validated MREs.</p><p>^a SNP effect on miRNA binding: D disrupts an MRE and C creates an MRE.</p><p>^b MAF is based on 1000G pilot 1 CEU population.</p><p>^c Number of <i>cis</i>-eQTL SNPs from the LD block (R² = 1, 1000G pilot 1, CEU)</p><p>^d Z-scores from a recent meta-analysis [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141351#pone.0141351.ref021" target="_blank">21</a>] are averaged for LD block (R² = 1); FDR < 0.05 for all associations.</p><p>^e Association type: C-concordant; U-unconcordant.</p><p>Top 30 filtered SNP-miR-probe associations, sorted based on their context+ scores.</p

MRE-SNPs from the filtered set of associations that overlap with validated miRNA-target interactions.

<p>* SNP has been experimentally shown to influence MRE.</p><p>^a SNP effect on miRNA binding: D disrupts an MRE and C creates an MRE.</p><p>^b MAF is based on 1000G pilot 1 CEU population.</p><p>^c Z-scores from a recent eQTL meta-analysis [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141351#pone.0141351.ref021" target="_blank">21</a>] are averaged for LD block (R² = 1, 1000G pilot 1, CEU); FDR < 0.05 for all associations.</p><p>^d Conservation shows in which species a corresponding MRE is present (polymiRTS v3.0 database).</p><p>^e Supported by AGO-CLIP data.</p><p>^f Validation method: LU- luciferase reporter assay; IM- immunoprecipitation; EX- target expression profiling; CL- CLASH; QP- qRT-PCR; SE- sequencing; PS- pSiLAC; and WE- Western blot.</p><p>^g Association type: C-concordant; U-unconcordant.</p><p>MRE-SNPs from the filtered set of associations that overlap with validated miRNA-target interactions.</p

Regional LD plots for the four C-type MRE-SNPs overlapping with the GWAS Catalog.

<p>Regional LD plots for the four C-type MRE-SNPs overlapping with the GWAS Catalog.</p

Graphs depicting miRNA-SNP-mRNA associations.

<p>Shown is an example subset of filtered associations supported by AGO-CLIP data (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141351#pone.0141351.s005" target="_blank">S4 Fig</a> for full data). The color of miRNA-SNP links shows miRNA targeting probability, assessed by TargetScan context+ score change (grey, context+ score change > 0; the gradient from yellow to red shows the magnitude of context+ score change) and the line type indicates concordance with the mechanism of miRNA-mediated regulation: a continuous line is concordant (C-type), and a dashed line is unconcordant (U-type). In the case of SNP-gene links, the concordance type is indicated by the color: a red line is C-type, a blue line is U-type, and the intensity of the color indicates the <i>cis</i>-eQTL effect size (overall Z-score) from the Westra <i>et al</i>. meta-analysis [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141351#pone.0141351.ref021" target="_blank">21</a>], averaged over all detected SNPs in the LD block (R² = 1). Multiple interactions between one SNP and one gene show several Illumina probes detecting the same transcript. Outlined genes are validated targets of a targeting miRNA, as reported by miRTarBase, TarBase, or miRecords.</p

MRE-SNPs in the <i>ISCU</i> and <i>MDM4</i> genes.

<p>(a), (d) A schematic depiction of each gene locus. Tracks denote the genomic region, SNP positions, AGO binding sites from starBase, most prevalent RefSeq transcript isoform, miRNA target sites from TargetScan v6.2, and Illumina detection probes. The region with the <i>cis</i>-eQTL MRE-SNP and affected probe (marked red) is expanded. (b), (e) Allelic expression pattern in the EGCUT sample set. Log-transformed and quantile-normalized expression values are visualized as boxplots, and individual expression values are depicted as points. On the boxplots, the line indicates median, box defines 25% - 75% quartiles and whiskers extend the data to 1.5× of interquartile range. (c), (f) MRE-SNP effects on miRNA binding. Vertical lines indicate canonical pairing, colons depict G:U wobble, and "x" denotes a mismatch. The miRNA seed region is shown in blue, and the MRE-SNP minor allele and its effect on miRNA binding is shown in red.</p

Age-related measurement invariance in the NEO-PI-3 facets: the changes in Comparative Fit Indices and Root Mean Square Error of Approximation values as a result of imposing increasingly strict parameter constraints in the measurement models of different age groups.

<p>Age-related measurement invariance in the NEO-PI-3 facets: the changes in Comparative Fit Indices and Root Mean Square Error of Approximation values as a result of imposing increasingly strict parameter constraints in the measurement models of different age groups.</p

The number of people in each age group.

<p>The number of people in each age group.</p

Latent trait scores of three facets and scores of single items that had their intercept equality constraints relaxed to obtain partial strong measurement invariance.

<p>Horizontal axis represents 12 age groups. Vertical axis represents the mean age group scores (in the standard deviation units of the youngest group).</p

Age differences in the 30 NEO-PI-3 facets before (dashed lines) and and after (solid lines) establishing partial measurement invariance.

<p>Horizontal axis represents 12 age groups. Vertical axis represents the mean age group scores (in the standard deviation units of the youngest group).</p