20 research outputs found
Statistical power of phylo-HMM for evolutionarily conserved element detection-5
<p><b>Copyright information:</b></p><p>Taken from "Statistical power of phylo-HMM for evolutionarily conserved element detection"</p><p>http://www.biomedcentral.com/1471-2105/8/374</p><p>BMC Bioinformatics 2007;8():374-374.</p><p>Published online 5 Oct 2007</p><p>PMCID:PMC2194792.</p><p></p>ample "0.0510" means = 0.05 and = 10. The points are their power at posterior probability threshold equal to 0.5. The point corresponding to the baseline (P0.25L50) is indicated as a green dot. The blue solid lines connect the points with the same , while the red dashed line connects the points with the same . Some of the points are highlighted by crosses. The green dotted line crosses show the 1-to-3quartile range. The black solid line crosses show the 95% bootstrap confidence interval of the median sensitivity and specificity
Statistical power of phylo-HMM for evolutionarily conserved element detection-7
<p><b>Copyright information:</b></p><p>Taken from "Statistical power of phylo-HMM for evolutionarily conserved element detection"</p><p>http://www.biomedcentral.com/1471-2105/8/374</p><p>BMC Bioinformatics 2007;8():374-374.</p><p>Published online 5 Oct 2007</p><p>PMCID:PMC2194792.</p><p></p>etic tree. The different lines represent the different branches as illustrated in the legend. (B) Relationships for branches in the symmetric star-topology tree. The different lines correspond to the different numbers of genomes (n) represented by the tree
Genome Scan for Gonadal Fat Mass
<div><p>(A) Animals were genotyped at an average 1.5 cM density using 1,032 SNPs polymorphic between the parental strains. LOD scores computed using sex as an additive covariate (black) failed to detect significant linkage. A genome scan accounting for interactions between sex and QTL (red) showed evidence for suggestive linkage on Chromosome 1 and significant linkage on Chromosomes 3, 5, 11, and 19. Dashed and solid lines are thresholds for suggestive (<i>p</i> < 1 × 10<sup>−3</sup>) and significant linkage (<i>p</i> < 5 × 10<sup>−5</sup>), respectively.</p><p>(B) Genome scans for gonadal fat mass using different models over mouse Chromosome 5. Scans for fat mass using all animals with (black) and without (green) sex as an additive covariate failed to detect significant linkage. Females analyzed alone (magenta) showed evidence for suggestive linkage (<i>p</i> < 2 × 10<sup>−4</sup>). When both sexes were analyzed to account for sex effects (red), a significant QTL was realized (<i>p</i> < 10<sup>−6</sup>).</p><p>For clarity, only the model incorporating both the “sex*add” and “sex*dom” terms is shown in red, although additional models incorporating the terms separately were also computed.</p></div
Properties of All Liver eQTLs
<div><p>(A) Distribution of all significant liver eQTLs across the genome in 2-cM bins. A total of 6,676 significant eQTLs were realized, representing 4,998 liver transcripts. Hotspots of nonrandom eQTL colocalization are clearly evident.</p><p>(B) Distribution of eQTLs with significant sex-specific effects. A total of 1,166 eQTLs representing 1,044 transcripts show an eQTL hotspot on Chromosome 5.</p><p>(C) Properties of eQTLs at increasing significance levels. As the threshold for significant linkage increases (<i>p</i>-value decreases, or LOD score increases), the proportion of <i>cis</i>-eQTLs (black) increases. The fraction of all eQTLs with sex effects (red) and <i>cis</i>-eQTLs with sex effects (blue) remains relatively constant at increasing thresholds. The dashed line indicates the genome-wide significance threshold (<i>p</i> < 5 × 10<sup>−5</sup>; genome-wide <i>p</i> < 0.05).</p><p>(D) Properties of sex-specific eQTLs at increasing significance levels. For eQTLs with significant sex effects, as with all eQTLs, the proportion of <i>cis</i>-eQTLs (black) increases and <i>trans</i> (blue) decreases as the threshold for significance increases. At the genome-wide threshold for significance (dashed line), over 70% of eQTLs with significant sex effects are <i>trans.</i></p></div
The Effects of Sex on <i>Trans</i>-eQTL Correlated with Gonadal Fat Mass
<div><p>(A) Example of the effect of genotype at a <i>trans</i> locus on gene expression. Presence of homozygous B6 (BB), C3H (CC), or heterozygous (BC) genotype at a <i>trans</i> locus affects transcript MMT00016118 levels (reported as mlratio) in a sex-specific manner, with effects detectable only in females. Coefficients of determination (<i>R</i><sup>2</sup>, or proportion variance explained) are shown along with associated ANOVA <i>p</i>-values. Several <i>trans</i>-eQTLs correlated with gonadal fat mass localize to regions overlapping with cQTLs for this trait, specifically, to Chromosome 19, 40 cM.</p><p>(B) For Chromosome 19, the vast majority of these correlated <i>trans</i>-eQTLs are biased toward larger effects on gene expression in females (red lines). The effect of any given <i>trans</i>-eQTL is approximated as <i>R</i><sup>2</sup> determined in a manner similar to that depicted in (A).</p></div
Heat Map of Liver Gene Expression
<p>Over 2,300 of the most differentially expressed genes in liver hierarchically clustered by animals (<i>x</i>-axis) against transcript levels (<i>y</i>-axis). Expression is reported as mlratio of individual experiment against a common pool. Red is over- and green underrepresented relative to pool.</p
Effect of Genotype on Fat Mass
<p>Homozygous B6 (BB), C3H (CC), or heterozygous (BC) genotype at all five QTL positions, separated by sex, are shown. The underlying genotypic effects of the QTLs on fat mass differ between the sexes. Coefficients of determination (<i>R</i><sup>2</sup>) are shown along with associated ANOVAs *<i>p</i> < 0.05, **<i>p</i> < 0.01, ***<i>p</i> < 0.001.</p
Relating the Gene Significance Measure for Weight (GSweight) to Genetic and Network Based Variables of the Blue Module
<div><p>(A) Scatterplot between GSweight (<i>y</i>-axis) and intramodular connectivity (k<sub>me</sub>) based on the module eigengene (<i>x</i>-axis). Each point corresponds to a gene in the Blue module.</p><p>(B) Scatterplot between GSweight (<i>y</i>-axis) and the sum of the mQTL significance measures of Chromosomes 2, 5, and 10 (GSmQTL* = GSmQTL2 + GSmQTL5 + GSmQTL10a).</p><p>(C) Scatterplot between GSweight (<i>y</i>-axis) and the mQTL significance measure of Chromosome 19 (GSmQTL19).</p><p>(D) Scatterplot between GSweight (<i>y</i>-axis) and the predicted value based on a multivariable regression model involving intramodular connectivity (k<sub>me</sub>) and the aforementioned mQTL significance measures (GSmQTL* and GSmQTL19). The linear regression model explains 70% of the variation in GSweight.</p><p>(E) Boxplot for visualizing the effect of the module based variables on GSweight. The 8 different boxplots correspond to the eight groups of genes that result by splitting the module variables by their median values. Genes with high/low GSmQTL* values are labeled by q+ and q−, respectively. Genes with high/low GSmQTL19 values are labeled by 19+ and 19−, respectively. Genes with high/low connectivity values are labeled by k+ and k−, respectively (For example, the boxplot labeled q+ 19− k− plots the GSweight distribution of the Blue module genes with a high GSmQTL*, a low GSmQTL19, and a low connectivity).</p></div
The Relationship between the Blue Module and Several Clinical Traits
<div><p>Module significance is defined as the mean of the absolute value of the correlation coefficient for all genes within a module with a physiological trait of interest. A module significance of 0.30 is statistically significant at a <i>p</i>-value of 0.05 for any module given <i>n</i> = 135 mice after correction for multiple comparisons (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020130#s4" target="_blank">Materials and Methods</a>).</p><p>Abfat, abdominal fat (g); Aneurysm, aneurysms as measured by histological examination using a semi-quantitative scoring method. AorticCal.L, aortic calcification in the lesion area; AorticCal.M, medial aortic calcification; Chol, total plasma cholesterol (mg/dl); FFA, plasma free fatty acids (mg/dl); HDL, high-density lipoprotein fraction of cholesterol (mg/dl); Index, adiposity index (total fat × 100/weight); Ins, plasma insulin (μg/l); LDL+VLDL, plasma low-density lipoprotein and very low-density lipoprotein choleseterol (mg/dl); Lesion, aortic lesion size as measured by histological examination using a semi-quantitative scoring method; MCP-1, plasma MCP-1 protein levels; otherfat, subcutaneous, retroperitoneal, and mesenteric fat (g); TG, plasma triglycerides (mg/dl); Totalfat, Abfat + otherfat; UC, plasma unesterified cholesterol (mg/dl).</p></div
Exon and junction microarrays detect widespread mouse strain- and sex-bias expression differences-0
Iled explanation of each set.<p><b>Copyright information:</b></p><p>Taken from "Exon and junction microarrays detect widespread mouse strain- and sex-bias expression differences"</p><p>http://www.biomedcentral.com/1471-2164/9/273</p><p>BMC Genomics 2008;9():273-273.</p><p>Published online 4 Jun 2008</p><p>PMCID:PMC2432077.</p><p></p