Illustration of the Mendelian randomization framework.

<p>In Mendelian randomization, if there is a causal effect of the exposure (e.g., smoking heaviness) that is being captured by the genotype on the outcome (e.g., lung cancer), then an association of genotype with the outcome should be detectable in a sufficiently large unstratified GWAS (panel A). This can be confirmed in a stratified analysis, where an association of genotype with the outcome should only be seen in the exposed group (i.e., smokers, panel B) and not the unexposed group (i.e., never-smokers, panel C). This is a special case of gene × environment (G × E) interaction, where both G and E are known, although it will not always be possible to stratify on the exposure, and stratification (which can be considered a form of statistical adjustment) can introduce other potential biases in certain circumstances (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005765#pgen.1005765.box003" target="_blank">Box 3</a>).</p

GxG loci detected by sparse partitioning.

<p>GxG loci detected by sparse partitioning.</p

Additional file 3: of Deep genome sequencing and variation analysis of 13 inbred mouse strains defines candidate phenotypic alleles, private variation and homozygous truncating mutations

Pairwise variant comparisons. The number of SNPs and indels shared between any two strains contained in the MGP variation catalogue. (XLSX 24 kb

Proportion of phenotypic variance explained by GxS versus by main effects.

<p>For the 15 phenotypes that had a GxS QTL, this plot depicts the percentage of phenotypic variance explained by models where sex was permitted to act as a main effect only relative to when it could act as a both main effect and interaction term. As detailed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096450#pone-0096450-t003" target="_blank">Table 3</a>, allowing GxS interaction effects in the model at least marginally improved the amount of phenotypic variance explained by predictors. Thus, all the points fall above the grey line, x = y. It is clear from the figure that adrenal gland weight (“aw”) had the greatest improvement in its variance explained by allowing interacting predictors (difference of 1.6%). Additional non-trivial abbreviations are as follows: chloride (“Cl”), triglycerides (“tg”), time spent frozen in fearful context (“c”), time spent frozen after fearful cue (“CuF”), startle response (“FPS”), area of glucose response curve (“ga”), B220+ cell percentage (“B”), and boli produced in the open field test (“b”). ALT occupied nearly the same position as chloride so is represented by the same symbol (“Cl”).</p

Main effects of sex on 55 heterogeneous stock mouse phenotypes.

<p>The vertical axis is the percent of variation explained. The ten largest effects are labeled.</p

Histogram of the posterior probabilities of the GxS QTLs found by Sparse Partitioning.

<p>This histogram illustrates the frequency all GxS interaction QTL identified by SP with a posterior probability above the .20 threshold.</p

Histogram of the posterior probabilities of the main effect QTLs found by Sparse Partitioning.

<p>This histogram includes all main effect QTLs identified by Sparse Partitioning with a posterior probability greater than .05. The horizontal red line at .20 represents the threshold we selected: QTL above it were retained.</p

Euphoria longana Lam.

原著和名: リウガン科名: ムクロジ科 = Sapindaceae採集地: 鹿児島県 肝属郡 佐多町 伊座敷 (大隅 肝属郡 佐多町 伊座敷)採集日: 1957/7/10採集者: 萩庭丈壽整理番号: JH026103国立科学博物館整理番号: TNS-VS-97610

Additional file 6: of Deep genome sequencing and variation analysis of 13 inbred mouse strains defines candidate phenotypic alleles, private variation and homozygous truncating mutations

Private SNPs with multiple VEP consequences. Private SNPs with multiple predicted VEP consequences for each strain strain. Consequence predictions are based on gene models obtained from Ensembl 78. (TXT 66669 kb

Hierarchy of evidence.

<p>Hierarchy of evidence.</p