Additional file 1: Figure S1. of Collaborative cross mice in a genetic association study reveal new candidate genes for bone microarchitecture

Phenotypic diversity between the CC lines. (A) phenotypic distribution among males and (B) females. From top-left, counter-clockwise: trabecular bone volume fraction (BV/TV; %), trabecular number (Tb.N; mm-1), thickness (Tb.Th; mm), and connectivity density (Conn.D; mm-3). (DOC 400 kb

Boletín de Segovia: Número 18 - 1895 febrero 11

Copia digital. Madrid : Ministerio de Cultura. Subdirección General de Coordinación Bibliotecaria, 200

GxG loci detected by sparse partitioning.

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

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

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

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

Additional file 4: of Identification of new loci involved in the host susceptibility to Salmonella Typhimurium in collaborative cross mice

Figure S3. Founder contributions and haplotype around Stsl4 QTL on Chr 6. (A) Genome scan magnification for Stsl4 QTL region (60–100 Mb on Chr 6). The mouse genome location is on the X-axis and significance (−log10(P)) values on the Y-axis, with genome-wide thresholds of association at E < 0.5, E < 0.1 and E < 0.05 levels indicated respectively by the gray, orange and red lines. Peak location (maximum value of –log10(P)) is marked by a star. (B) Founder contributions in the same magnified region. The peak location is marked by a star. Each of the 8 founders is in a different color. The mouse genome location is on the X-axis and Y-axis shows the founder estimated effect on splenic bacterial load after S. Typhimurium infection. (C) Founder contributions at Stsl4 QTL peak (81.2 Mb). X-axis shows the different founder strains. Y-axis shows the estimated founder effect. No obvious contributions explain Stsl4 QTL, but B6 has the lowest estimated impact while NZO/HILtJ and PWK/PhJ have the highest estimates. (PDF 160 kb

Additional file 7: of Identification of new loci involved in the host susceptibility to Salmonella Typhimurium in collaborative cross mice

Table S3. Genes remaining in Stls2 interval post merge analysis. Gene symbol, start and end positions, name, high merged SNPs, expression in immune cell, cell-type major expression and Gene Ontology (GO) terms are given. Gene positions (build mm9), names as well as GO terms were collected from UCSC, MGI and ENSEMBL, while expression data were collected from Male/Female RNAseq of ImmGen. (XLSX 492 kb

Additional file 3: of Identification of new loci involved in the host susceptibility to Salmonella Typhimurium in collaborative cross mice

Figure S2. Founder contributions and haplotype around Stsl3 QTL on Chr 1. (A) Genome scan magnification for Stsl3 QTL region (70–100 Mb on Chr 1). The mouse genome location is on the X-axis and significance (−log10(P)) values on the Y-axis, with genome-wide thresholds of association at E < 0.5, E < 0.1 and E < 0.05 levels indicated respectively by the gray, orange and red lines. Peak locations Stsl3a and Stsl3b (maximum value of –log10(P)) are marked by stars. (B) Founder contributions in the same magnified region. The peak location of Stsl3a is marked by a star. Each of the 8 founders is in a different color. The mouse genome location is on the X-axis and Y-axis shows the founder estimated effect on splenic bacterial load after S. Typhimurium infection. (C) Founder contributions at Stsl3a QTL peak (83.9 Mb). X-axis shows the different founder strains. Y-axis shows the estimated founder effect. No obvious contributions explain Stsl3a QTL, but B6 (grey) has the highest estimated impact of the 8 founders. (D) Founder contributions at Stsl3b QTL peak (79.2 Mb). There is no obvious founder contribution for Stsl3b QTL peak region. 129 (pink) has the highest estimated impact of the 8 founders while PWK (red) has the lowest estimate. (PDF 215 kb