Venn diagram indicating numbers of probes sharing differential expression (q-values 0

<p><b>Copyright information:</b></p><p>Taken from "Differential gene expression in femoral bone from red junglefowl and domestic chicken, differing for bone phenotypic traits"</p><p>http://www.biomedcentral.com/1471-2164/8/208</p><p>BMC Genomics 2007;8():208-208.</p><p>Published online 2 Jul 2007</p><p>PMCID:PMC1934367.</p><p></p>015) in sex specific contrasts between WL and RJ and in contrast between all WL and all RJ). Numbers within shared fields of circles indicate the number of probes exhibiting DE in overlapping contrasts

Comparison of results obtained by microarray-analysis and by qPCR-analysis

<p><b>Copyright information:</b></p><p>Taken from "Differential gene expression in femoral bone from red junglefowl and domestic chicken, differing for bone phenotypic traits"</p><p>http://www.biomedcentral.com/1471-2164/8/208</p><p>BMC Genomics 2007;8():208-208.</p><p>Published online 2 Jul 2007</p><p>PMCID:PMC1934367.</p><p></p> On y-axis, positive M-values indicate more expression in WL, whereas negative M-values indicate more expression in RJ. Nine genes included in qPCR-analysis are presented along x-axis. To indicate statistical significance in real-time PCR at the p < 0.05 level the * symbol is used. To indicate q-values < 0.015 in the microarray analysis the ‡ symbol is used

Hierarchical clustering of microarray data for 85 microarray probes showing differential expression in all three contrasts performed between red junglefowl and White Leghorn

<p><b>Copyright information:</b></p><p>Taken from "Differential gene expression in femoral bone from red junglefowl and domestic chicken, differing for bone phenotypic traits"</p><p>http://www.biomedcentral.com/1471-2164/8/208</p><p>BMC Genomics 2007;8():208-208.</p><p>Published online 2 Jul 2007</p><p>PMCID:PMC1934367.</p><p></p> Individuals (five of each sex and line) are scattered along the x-axis and probes are distributed along the y-axis. For each individual and probe, colors represent log2(sample fluorescence/reference fluorescence) according so upper scale bar (red indicates more expression in sample channel whereas green indicate more expression in reference channel). Hierarchical clustering was performed using the Euclidean metric

Results derived from quantitative PCR analysis of six transcripts expressed higher levels in the red junglefowl in the microarray analysis

<p><b>Copyright information:</b></p><p>Taken from "Differential gene expression in femoral bone from red junglefowl and domestic chicken, differing for bone phenotypic traits"</p><p>http://www.biomedcentral.com/1471-2164/8/208</p><p>BMC Genomics 2007;8():208-208.</p><p>Published online 2 Jul 2007</p><p>PMCID:PMC1934367.</p><p></p> Chicken individuals are presented along the x-axis: WLM = White Leghorn male, WLF = White Leghorn female, RJM = red junglefowl male, RJF = red junglefowl female. For each transcript, expression relative to GAPDH-expression is presented on the y-axis. Error bars indicate standard deviations

Relative expression values of differentially expressed transcripts located in QTL-regions

<p><b>Copyright information:</b></p><p>Taken from "Differential gene expression in femoral bone from red junglefowl and domestic chicken, differing for bone phenotypic traits"</p><p>http://www.biomedcentral.com/1471-2164/8/208</p><p>BMC Genomics 2007;8():208-208.</p><p>Published online 2 Jul 2007</p><p>PMCID:PMC1934367.</p><p></p> Along each QTL-interval, directions of arrows visualize orientation of expression (i.e. sense or antisense strand). Arrow colors visualize direction and magnitude of log2(sample channel fluorescence/reference channel fluorescence) according to upper scale bar. Red arrows indicate more expression in sample than in reference whereas green arrows indicate more expression in reference

Results derived from quantitative PCR analysis of three transcripts expressed higher levels in the White Leghorn in the microarray analysis

<p><b>Copyright information:</b></p><p>Taken from "Differential gene expression in femoral bone from red junglefowl and domestic chicken, differing for bone phenotypic traits"</p><p>http://www.biomedcentral.com/1471-2164/8/208</p><p>BMC Genomics 2007;8():208-208.</p><p>Published online 2 Jul 2007</p><p>PMCID:PMC1934367.</p><p></p> Chicken individuals are presented along the x-axis: WLM = White Leghorn male, WLF = White Leghorn female, RJM = red junglefowl male, RJF = red junglefowl female. For each transcript, expression relative to GAPDH-expression is presented on the y-axis. Error bars indicate standard deviations

Heat map illustrating expression ratios (log2(sample fluorescence/reference fluorescence)) for probes from enriched Gene Ontology categories GO:0005842 and GO:0005843, representing cytosolic large and small large ribosomal subunits, respectively

<p><b>Copyright information:</b></p><p>Taken from "Differential gene expression in femoral bone from red junglefowl and domestic chicken, differing for bone phenotypic traits"</p><p>http://www.biomedcentral.com/1471-2164/8/208</p><p>BMC Genomics 2007;8():208-208.</p><p>Published online 2 Jul 2007</p><p>PMCID:PMC1934367.</p><p></p> WLM = White Leghorn males, WLF = White Leghorn females, RJM = red junglefowl males, RJF = red junglefowl females. Red colored squares indicate more expression in sample than in reference whereas green indicate more expression in reference

Volcano plots illustrating distributions of M- and -log(FDR-adjusted p-values) for all probes on microarray in three contrasts between WL and RJ

<p><b>Copyright information:</b></p><p>Taken from "Differential gene expression in femoral bone from red junglefowl and domestic chicken, differing for bone phenotypic traits"</p><p>http://www.biomedcentral.com/1471-2164/8/208</p><p>BMC Genomics 2007;8():208-208.</p><p>Published online 2 Jul 2007</p><p>PMCID:PMC1934367.</p><p></p> Horizontal red lines indicate DE significance threshold (q = 0.015) and vertical red lines indicate M-values of 1 and -1. Positive M-values indicate higher expression in WL

A PCR-based diagnostic test reveals complete association of a duplication junction point with the Duplex-comb phenotypes in chickens.

<p>Samples from the Caumont, Crevecoeur and Padova breeds were supplied by INRA, some of which were part of the AvianDiv Project [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004947#pgen.1004947.ref038" target="_blank">38</a>]. All other samples were collected in the USA except for Sicilian Buttercup and Houdan, which were collected in both countries.</p><p>A PCR-based diagnostic test reveals complete association of a duplication junction point with the Duplex-comb phenotypes in chickens.</p

The Duplex-comb phenotypes V-shaped and Buttercup are both associated with a novel 20 Kb duplication on chicken chromosome 2.

<p>(A) Phenotypes associated with the <i>Duplex-comb</i> locus V-shaped (<i>D*V</i>), Buttercup (<i>D*C</i>) and wild-type (<i>D*N</i>) single comb alleles. (B) A 381 Kb haplotype is IBD in <i>D*V</i> individuals, SNP names in the region marked in red. Yellow shading represents heterozygous genotypes with blue/orange representing reciprocal homozygous genotypes. Genotype data is from the 60K SNP chip and color coded according to genotype with missing data shown in black. A single SNP GGaluGA142157 at 38,806,246 bp (marked in yellow) is heterozygous in all <i>D*V</i> individuals, suggestive of a duplication. A broader view of haplotypes in more individuals is available in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004947#pgen.1004947.s001" target="_blank">S1 Fig.</a> (C) A TaqMan assay was used to investigate the genomic copy number of the putative duplicated region, showing that a duplication is present in both <i>D*V</i> and <i>D*C</i> individuals. Each bar represents a single individual. Error bars represent the minimum and maximum estimated copy number as calculated from technical replicates of each sample by Copy Caller software (ABI). (D) The <i>Duplex-comb</i> alleles are associated with a tandem duplication with no sequence homology at the junction point. The middle line shows the sequence at the junction point with vertical dashes indicating sequence alignment to the 5’ (bottom line) and 3’ (top line) boundaries of the duplicated region. A LTR element is shaded in gray.</p