22 research outputs found

    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

    A matrix of plots illustrating the agreement of HRV between three time points.

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    <p>The upper right panels consist of scatterplots with identity line (45¬į line though the origin). The lower left panels consist of Bland-Altman plots with confidence bounds and bias (dotted red line) and the horizontal black line passing through the origin. The confidence bounds show the mean of the difference between time points plus or minus twice of the standard deviation of the difference.</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‚Äďsymptom score; GAF-F, Global Assessment of Functioning‚Äďfunction 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

    Protein-protein interaction network build from proteins encoded in associated intervals.

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    <p>The colored, full circles represent proteins encoded in associated intervals (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122501#pone.0122501.s002" target="_blank">S2 Table</a>). The smaller, grey circles represent interactors of indirect connections. Functionally, the DAPPLE-constructed diagram can be divided into two main groups: group ‚ÄúA‚ÄĚ mostly involved in the regulation of gene expression and inflammation; and group ‚ÄúB‚ÄĚ mostly involved in cell adhesion.</p

    Region-specific gene expression profiles in each lobe.

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    <p>A) The majority of genes were ubiquitously expressed in the cortical surface areas of all four lobes of the brain. A small percentage of the genes were either distinctively expressed in one lobe or co-expressed in multiple but not all four lobes of the brain. The frontal lobe exhibits the most distinctively expressed genes. See <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006143#pgen.1006143.s006" target="_blank">S5 Table</a> for the lists of genes and locations. B) The distribution of functional annotations of the transcripts distinctively expressed in the frontal lobe. ‚ÄúAll‚ÄĚ indicates the distribution of all transcripts included in our analysis, irrespective of their expression levels and anatomical locations. There are a higher proportion of intergenic transcripts in the frontal lobe (22% compared to 14%). C) A gene network analysis for the frontal lobe (excluding intergenic transcripts). The yellow-colored genes belong to the most significantly associated pathway: interferon-gamma-mediated signaling pathway, related to immunity (FDR = 3.2 x10<sup>-4</sup>). Half of the genes were originally from the transcripts distinctively expressed in the frontal lobe. See <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006143#pgen.1006143.s008" target="_blank">S7 Table</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006143#pgen.1006143.s009" target="_blank">S8 Table</a> for the complete list of associated pathways.</p

    Applying the genetically based cortical parcellations to independent data.

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    <p>A) The phenotypic correlation matrix of VETSA twin cohort versus the phenotypic correlation matrix of combined-5-cohort (C5C). The Mantel test confirmed that the similarity between them was highly significant (<i>p</i> = 0.0001). B) Cortical brain phenotypes‚ÄĒsurface area measures of 12 cortical regions after controlling for total surface area. The cortex was parceled into 12 genetically based regions of maximal shared genetic influence derived from the VETSA sample [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006143#pgen.1006143.ref016" target="_blank">16</a>]. 1. motor & premotor; 2. dorsolateral prefrontal; 3. dorsomedial frontal; 4. orbitofrontal; 5. pars opercularis & subcentral; 6. superior temporal; 7. posterolateral temporal; 8. anteromedial temporal; 9. inferior parietal; 10. superior parietal; 11. precuneus; 12. occipital. C) The phenotypic correlation versus the genetic correlations (<i>r</i><sub><i>g</i></sub>) matrices of VETSA. The correlation of the two matrices was also highly significant (<i>p</i> < 0.0001), suggesting high genetic contributions to the cortical patterning. Correlation coefficients are listed in Supplemental <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006143#pgen.1006143.s002" target="_blank">S1 Table</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006143#pgen.1006143.s003" target="_blank">S2 Table</a>.</p
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