Most differentially regulated transcripts in thymus as identified by IPA microarray analysis.

<p>^a Networks identified by Ingenuity pathway Analysis are included in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134866#pone.0134866.s001" target="_blank">S1 File</a>.</p><p>Most differentially regulated transcripts in thymus as identified by IPA microarray analysis.</p

Ingenuity pathway analysis showing the most highly scoring canonical pathways (according to <i>P</i> value) associated with the response of thymocytes to CAV infection.

<p>Five pathways had a <i>P</i> value < 0.05. The orange line represents the ratio of the number of differentially expressed thymus genes in a particular pathway whose expression is correlated with cellular response towards CAV divided by the total number of genes that make up that pathway. Blue bars represent the <i>P</i> value for each pathway and are expressed as -1 times the log of the <i>P</i> value. The threshold line corresponds to a <i>P</i> value of 0.05.</p

Pathogenicity evaluations of infected, uninfected and mock-infected animals at day 14 post-infection.

<p><i>a</i> Anaemia is defined as a hematocrit value of less than 27.</p><p><i>b</i> The six most affected chicks, based on haematocrit values, were used for microarray analysis.</p><p>Gross pathological examination of the thymuses and bone marrows was performed in a blind manner, and a clinical score was estimated by scoring the severity of the thymus atrophy and paleness of the bone marrow, as 0, 1 or 2.</p

qRT-PCR mRNA expression levels to confirm microarray results following CAV infection in different lymphoid tissues.

<p>¹Mean fold difference between infected and mock-infected birds at each time-point (n = 5 (6 for d 14)); <i>P</i><0.05, positive values are up-regulated in infected birds and negative values are down-regulated in infected birds.—: no significant difference between groups or mRNA not expressed in one or both groups. Changes greater than three-fold are highlighted in bold.</p><p>qRT-PCR mRNA expression levels to confirm microarray results following CAV infection in different lymphoid tissues.</p

T-cell receptor signalling was the most significant gene network of over-expressed genes in infected samples of thymus as identified by Ingenuity Pathway Analysis (www.ingenuity.com).

<p>Colored nodes represent differentially regulated genes (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134866#pone.0134866.t004" target="_blank">Table 4</a>) while genes in uncolored nodes were not identified as differentially expressed and were integrated into the computationally generated network indicating a relevance to it (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134866#pone.0134866.s001" target="_blank">S1 File</a>). T-cell receptor signalling gene relationships were overlaid to the network. Solid interconnecting lines represent genes directly connected and dotted lines signify the indirect connection between genes and cellular functions. Top functions of the genes were related to T-cell receptor signalling, immune response and cellular assembly and death, identified around the MALT1 gene (in red). Node shapes represent different biological molecules.</p

Summary statistics of the pooled heterozygosity metric for selection signature in candidate genes.

<p>Summary statistics of the pooled heterozygosity metric for selection signature in candidate genes.</p

A graphical comparison of two genome scanning strategies.

<p>sliding windows (SW) vs., creeping windows (CW). With SW a chromosome is split into non (or partly) overlapping windows of 40 K and while passing over genomic gaps, it may not perfectly overlie a selective sweep. CW implements an elevated resolution moving windows in steps of only one SNP forward. The approach bridges small (<10 K) gaps while it stops at larger gaps and re-starts at the opposite side. CW always centers a window relative to a sweep position.</p

Collected panel of genomic regions identified as candidate selective sweeps.

a<p>Positions in normal format represent “distinct sweeps” revealed by the <i>H_P</i> metric. A distinct sweep spans over numerous consecutive significant windows and depicts a typical valley of heterozygosity.</p>b<p>Signals overlapping genes with a previously described association.</p

Distribution patterns of the <i>H_P</i> profile from 862’400 windows creeping over the genome.

<p>Pink and blue densities represent, respectively, the observed and the panel of recorded lowest <i>H_P</i>-values from 10’000 re-sampling runs in real data. Windows with <i>H_P</i>≤0.252 represent significant signals at the empirical error level <i>P</i>≤0.001. As indicated, 1816 windows characterize 82 selected regions with a more extreme local homozygosity than expected under neutrality.</p

Histograms of (A) distance between neighboring markers and (B) gap size in the final data set.

<p>Histograms of (A) distance between neighboring markers and (B) gap size in the final data set.</p