A NeighborNet phylogenetic network of rat strains based on uncorrected p-distances of the genotypes of complete set of 820 markers

<p><b>Copyright information:</b></p><p>Taken from "A genome-wide SNP panel for mapping and association studies in the rat"</p><p>http://www.biomedcentral.com/1471-2164/9/95</p><p>BMC Genomics 2008;9():95-95.</p><p>Published online 25 Feb 2008</p><p>PMCID:PMC2266910.</p><p></p

Markers are sorted by chromosome and the position of the maker on that chromosome

Yellow indicates BN alleles, blue indicates polymorphic alleles as compared to BN and green positions indicate heterozygous genotypes. A hierarchical cluster tree, based on Wards algorithm is shown on top.<p><b>Copyright information:</b></p><p>Taken from "A genome-wide SNP panel for mapping and association studies in the rat"</p><p>http://www.biomedcentral.com/1471-2164/9/95</p><p>BMC Genomics 2008;9():95-95.</p><p>Published online 25 Feb 2008</p><p>PMCID:PMC2266910.</p><p></p

A Neighbor-joining phylogenetic tree of rat strains based on uncorrected p-distances of the genotypes of complete set of 820 markers

<p><b>Copyright information:</b></p><p>Taken from "A genome-wide SNP panel for mapping and association studies in the rat"</p><p>http://www.biomedcentral.com/1471-2164/9/95</p><p>BMC Genomics 2008;9():95-95.</p><p>Published online 25 Feb 2008</p><p>PMCID:PMC2266910.</p><p></p

A highly significant LOD score for the leptin receptor locus on chromosome 5 is obtained

<p><b>Copyright information:</b></p><p>Taken from "A genome-wide SNP panel for mapping and association studies in the rat"</p><p>http://www.biomedcentral.com/1471-2164/9/95</p><p>BMC Genomics 2008;9():95-95.</p><p>Published online 25 Feb 2008</p><p>PMCID:PMC2266910.</p><p></p

Comparison of the Haplotype Block Densities between Syntenic Regions of Rat, Mouse, and Human (Same Genome Segments as Shown in Figure 1)

<p>The scatter plots show log₁₀ of the amount of haplotype blocks per 100-kb bin in rat (horizontal) against log₁₀ of the amount of haplotype blocks seen in syntenic region of mouse (A) and human (B) genome (vertical). Data points for gene-containing and intergenic genomic bins are shown as closed and open blocks, respectively. Observed correlations of haplotype block densities are significant in linear (<i>r</i> = +0.5530; <i>p</i> < 0.0001 [A] and <i>r</i> = +0.4563; <i>p</i> = 0.0005 [B]) as well as in log-transformed space (<i>r</i> = +0.6795; <i>p</i> < 0.0001 [A] and <i>r</i> = +0.3209; <i>p</i> = 0.0180 [B]).</p

Analysis of LD Decay for Functionally Different Segments of the Human Genome

<div><p>(A) The graph shows average values of |D′| and their confidence limits (± standard deviation) as a function of the physical distance between SNPs for the following categories: (1) both SNPs reside in the same gene (blue line), (2) the SNPs reside in two different genes (green line), (3) both SNPs reside in the same intergenic region (red line), (4) one SNP resides in the gene and the other in the 30 kb upstream region of the same gene (purple line), and (5) one SNP resides in the gene and the other in the 30 kb downstream region of the same gene (gray line).</p><p>(B) Frequency distribution spectrum of |D′| values for SNP pairs at 100-kb distance. High |D′| values (>0.8) are overrepresented for equally spaced SNPs in a gene and its flanking regions as compared to intergenic regions.</p><p>(C) Frequency distribution of high LD values (|D′| > 0.5) for SNP pairs at 450-kb distance. Higher LD values are observed between a gene and its upstream region.</p><p>(D) Frequency distribution of high LD values (|D′| > 0.5) for SNP pairs at 650-kb distance. Higher LD values are observed between a gene and its upstream region.</p><p>The bin with |D′| = 1 is isolated to a separate bin in panels (B–D) as there is a considerable frequency bias for this |D′| value. Similar graphs plotted for separate human populations are available as <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020121#pgen-0020121-sg003" target="_blank">Figures S3</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020121#pgen-0020121-sg004" target="_blank">S4</a>, and S5.</p></div

Patterns of LD for Orthologous Genomic Segments of Approximately 5 Mb in Rat, Human, and Mouse

<p>LD plots for orthologous genomic segments in rat (A), human (B), and mouse (C) are shown. For each panel, the following information is shown: LD plot (top), haplotype blocks in SNP coordinates (middle), and physical map and haplotype blocks in physical coordinates (bottom). The haplotype map has a gradient representation for |D′| values that assists visual comparison of haplotype structure. Haplotype blocks were built with stringent criteria, sometimes resulting in splitting of visually recognized blocks. Three characteristic haplotype blocks that are conserved cross-species have been color-coded and are discussed in the text. Similar plots for a second mouse set, two other human populations, and the combined human set are available as <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020121#pgen-0020121-sg001" target="_blank">Figures S1</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020121#pgen-0020121-sg002" target="_blank">S2</a>.</p

A genome-wide screen for miRNAs that inhibit A375 melanoma cell growth.

<p>(A) Inhibition of melanoma growth was measured by means of cell viability and cell count. For each sample a B-score was calculated and B-scores from both assays are plotted against each other. There is a strong correlation between both assays. The B-scores for one miRNA, miR-518b, fell outside the range of the graph: they were −6 for cell count and −12 for cell viability. (B) A comparison with a normal distribution shows that the cell viability screen is sensitive for identifying growth-inhibitory miRNAs. A concomitant estimate of the false discovery rate is shown in grey fill (secondary axis). (C) 55 potential inhibitory miRNAs were tested in a confirmation screen against 11 empty vector samples and a population of 28 miRNAs with small or no effects in the primary screen. Box plots show values between 25^th and 75^th percentile in boxes, and the outermost values as whiskers. 20 of 55 inhibitory miRNAs scored better than any of the control miRNAs (below dashed line). *p = 6.8*10⁻⁵, **p = 1.6*10⁻⁶, ***p = 5.4*10⁻¹⁰. (D) Individual hits selected for follow-up, and their relative effect on cell viability. A virus containing a short-hairpin construct targeting BRAF was used as a positive control. Error bars represent standard deviation of three samples.</p

Effect of introduction of synthetic miRNAs on A375 viability.

<p>A375 cells were transfected with a range of concentrations of different miRNAs, and 72 hours after transfection viability was measured by means of MTS assay. Effects are compared to a scrambled control and a pool of 4 siRNAs against BRAF (siBRAF) as a positive control for A375 growth inhibition. Specific effects of miRNAs are best observed at concentrations of 10 nM. Each panel shows a different subset of miRNA mimics, although miRNAs were assessed in the same experiment. Error bars represent standard deviation of three samples. A representative of three experiments is shown.</p

Comparison of miRNA-induced effects in several melanoma cell lines.

<p>Cells were transfected with 10 nM (A375 and A2058) or 30 nM (SK-MEL-28 and SK-MEL-173) RNA and cell viability was measured 72 hours after transfection. Data are plotted relative to a mock-infected control. Error bars represent standard deviation of three samples.</p