30 research outputs found

    Figure 5

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    <p>A: Mean accuracy in the visual search task for the <i>CHRNA4</i> C- group versus the C+ group as a function of load condition. B: Mean of median reaction time in the visual search task for the <i>CHRNA4</i> C- group versus the C+ group as a function of load condition. Error bars represent standard error of the mean.</p

    Gene expression data of the Allen Human Brain Atlas were mapped onto the 12 genetically based cortical regions in the MR space.

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    <p>A) Resulting volume registration between FreeSurfer surface (fsaverage) and Allen brain MNI coordinates displayed as a point cloud, with a slice of the MRI imaging at the bottom (colin27). B) After the volume registration, gene expression data points are mapped to FreeSurfer surface vertices by assigning each surface vertex the gene expression of the closest (Euclidean distance) Allen brain data point using nearest neighbor interpolation. If two vertices have the same closest Allen brain data point, they belong to the same patch and the patch id is displayed as color. Thus, the color patches illustrate the local density of data points. The color patches with similar sizes across the cortex represent an even distribution of Allen brain data points and their surface correspondences. Colors of the dots in both (A) and (B) panels represent cortical regions to which they were assigned, corresponding to the color schemes in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006143#pgen.1006143.g001" target="_blank">Fig 1B</a>.</p

    Testing gene sets associated with normal neurocognitive variation for enrichment of association with schizophrenia.

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    <p><i>q</i>-value, obtained from 3 GSEA runs with 1,000 permutations each). The maximum standard deviation from the average <i>q</i>-value was 0.06. Sets that passed the enrichment threshold (<i>p</i>-value≤0.05, FDR <i>q</i>-value≤0.25) were tested for validation using random mimic sets (see Table S4 in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0081052#pone.0081052.s001" target="_blank">File S1</a>).<sup></sup> For each GWAS dataset the 5 most enriched candidate sets are shown. The rank position (R) of the gene set within the total number of gene sets tested was determined by the average false discovery rate (</p><p>% of the random sets (i.e. validated sets).<sup>a</sup> indicates sets that were more enriched than 98</p><p><sup>b</sup> indicates sets that did not pass the enrichment threshold but were among the 5 most enriched in the corresponding sample.</p><p>“n.e.”. Visuospatial attention.1 – Visuospatial attention task with valid cue to the location of the visual target; Visuospatial attention.3 – Visuospatial attention task with neutral cue to the location of the visual target. The number after each gene set name represents the number of genes within that set (e.g. the Colour-word interference −25 set contains the top 25 genes within the colour-word interference ranking list of genes).<sup></sup> Sets that did not pass the enrichment threshold and ranked outside the top 5 are indicated by </p

    Testing gene sets associated with normal neurocognitive variation for enrichment of association with bipolar disorder.

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    <p><i>q</i>-value, obtained from 3 GSEA runs with 1,000 permutations each). The maximum standard deviation from the average <i>q</i>-value was 0.07. Sets that passed the enrichment threshold (<i>p</i>-value≤0.05, FDR <i>q</i>-value≤0.25) were tested for validation using random mimic sets (see Table S4 in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0081052#pone.0081052.s001" target="_blank">File S1</a>).<sup></sup> For each GWAS dataset, the 5 most enriched candidate sets are shown. For the German dataset, the 14 most enriched sets are presented to show the overlap with the other datasets. The rank position (R) of the gene set within the total number of gene sets tested is determined by the average false discovery rate (</p><p>% of the random sets (i.e. validated sets).<sup>a</sup> indicates sets that were more enriched than 98</p><p><sup>b</sup> indicates sets that did not pass the enrichment threshold but were among the 5 most enriched in the corresponding sample.</p><p>“n.e.”. Visuospatial attention.1 – Visuospatial attention task with valid cue to the location of the visual target; Visuospatial attention.3 – Visuospatial attention task with neutral cue to the location of the visual target. The number after each gene set name represents the number of genes within that set (e.g. the Colour-word interference −25 set contains the top 25 genes within the colour-word interference ranking list of genes).<sup></sup> Sets that did not pass the enrichment threshold and ranked outside the top 5 are indicated by </p><p><i>p-</i>value of zero (0.0) indicates an actual <i>p</i>-value of less than 1/number-of-permutations.<sup></sup> A reported </p

    Genetic Sources Influencing Relational Complexity (RC) Underpin Intelligence and Covariation Between Reasoning and Working Memory.

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    <p>In this Cholesky decomposition [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0123886#pone.0123886.ref041" target="_blank">41</a>], additive genetic factors are designated A<sub>1</sub>-A<sub>4</sub>, and non-shared environmental factors E<sub>1</sub>-E<sub>4</sub> (dashed lines indicate non-significant pathways). Heritability (<i>h<sup>2</sup></i>) is shown for each trait. Parameter estimates are standardised such that when squared they indicate the percentage of variance accounted for (shown with 95% confidence intervals). Variable order was chosen to examine (i) the contribution of sources influencing RC (i.e. A<sub>1</sub>, E<sub>1</sub>) to the covariation between reasoning and working memory, and (ii) if sources influencing IQ added to this covariation independently of RC. For greater detail see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0123886#pone.0123886.s002" target="_blank">S2 Text</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0123886#pone.0123886.s001" target="_blank">S1 Fig</a> (focussing on covariation between RC and IQ) and S2 (showing alternative variable orders for the quadrivariate Cholesky). Note that unless there are qualitative sex differences, the order of traits in a Cholesky decomposition does not change measure of fit (or conclusion).</p

    Demographic data and clinical characterization of individuals participating in a faces matching functional MRI study.

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    <p>Abbreviations: BD, bipolar disorder; HC, healthy controls; SD, standard deviation; WASI, Wechsler Abbreviated Scale of Intelligence; IDS, Inventory of Depressive Symptoms; YMRS, Young Mania Rating Scale; PANSS P score, Positive and Negative Syndrome Scale positive subscale; GAF-S, Global Assessment of Functioning–symptom score; GAF-F, Global Assessment of Functioning–function score; BD PGRS, bipolar disorder polygenic risk score; ms, milliseconds.</p><p>BD PGRS values are reported as z-scores (with SD in brackets).</p><p>Complete behavioral data (response times and accuracy rates per condition) were available for 80/85 BD and 119/121 HC. For the remaining individuals (5 BD, 2 HC), an accuracy rate for each session (i.e. a combined rate for negative faces and shapes, and for positive faces and shapes) was available and was used to confirm that the participants paid attention to the task (accuracy rate: 97.4% and 96.0%, respectively).</p><p><sup>a</sup> Mean age at fMRI scanning. Age range was 18 to 63.</p><p><sup>b</sup> IDS score at scanning was available for 60/85 individuals (70.6%).</p><p><sup>c</sup> YMRS score at scanning was available for 69/85 individuals (81.2%).</p><p><sup>d</sup> PANSS P score at scanning was available for 38/85 individuals (44.7%).</p><p><sup>e</sup> Last six months</p><p>Demographic data and clinical characterization of individuals participating in a faces matching functional MRI study.</p

    GSEA of differentially expressed cortical genes in psychiatric disorders and non-psychiatric phenotypes.

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    <p>GSEA was used to analyse the differentially expressed cortical genes, as gene sets, for enrichment of association signal in three different BP GWASs (a German sample, the Norwegian TOP sample and the British WTCCC BP sample <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031687#pone.0031687-Cichon1" target="_blank">[20]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031687#pone.0031687-Djurovic1" target="_blank">[41]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031687#pone.0031687-WTCCC1" target="_blank">[42]</a>), three SCZ GWASs (the Norwegian TOP sample, the German part of a combined German-Dutch SCZ GWAS and a Danish sample <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031687#pone.0031687-Rietschel1" target="_blank">[19]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031687#pone.0031687-Athanasiu1" target="_blank">[43]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031687#pone.0031687-Ingason1" target="_blank">[44]</a>) and six non-psychiatric phenotypes (from WTCCC; CD: Crohn's disease, CHD: coronary heart disease, HT: hypertension, RA: rheumatoid arthritis, T1D: type 1 diabetes and T2D: type 2 diabetes, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031687#pone.0031687-WTCCC1" target="_blank">[42]</a>). The analysis was based on extraction of modified Sidak's minimum <i>P</i>-values <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031687#pone.0031687-Saccone1" target="_blank">[45]</a>, as implemented in LDsnpR. FDR q-value<0.1 was set as cut-off value for significant enrichment.</p>*<p>: One FMCx gene was not represented in the data set.</p>**<p>: Two FMCx genes were not represented in the data set.</p
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