The co-expression network where hubs are highlighted.

<p>The names are also given. The list of hubs is available in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060045#pone.0060045.s007" target="_blank">Table S1</a>.</p

Summary of the statistical pipeline.

<p>Data are represented in green (expression data and pH), statistical methods are represented in purple, results are represented in red.</p

Detailed display of cluster 4.

<p>Nodes that are influential for the partial correlation with pH, as well as nodes that are important for the structure of the graph (hubs, high betweenness), are highlighted. The other clusters are displayed similarly in Supplemental Material, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060045#pone.0060045.s001" target="_blank">Figures S1</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060045#pone.0060045.s002" target="_blank">S2</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060045#pone.0060045.s003" target="_blank">S3</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060045#pone.0060045.s004" target="_blank">S4</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060045#pone.0060045.s005" target="_blank">S5</a>, and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060045#pone.0060045.s006" target="_blank">S6</a>.</p

Boxplots of the partial correlations between the gene expressions and the pH for each cluster.

<p>Cluster 4 is significantly correlated with the pH phenotype (p-value is equal to 0.001).</p

The co-expression network where genes with high betweenness are highlighted.

<p>The names are also given. The list of genes with high betweenness is available in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060045#pone.0060045.s007" target="_blank">Table S1</a>.</p

Bibliographic network obtained with 10 pH-related genes.

<p>Pink nodes are the genes included in cluster 4; the other nodes are green. Finally, white nodes are the genes included by IPA to define the network but not shown to be regulated by an eQTL in our previous study.</p

Moran’s plot of the partial correlation between pH and expression levels in the co-expression network.

<p>Influential nodes are displayed in color and their names are given. Influential genes labeled “H–H” have a strong positive correlation with pH (above the mean) and are linked to genes having a strong positive correlation with pH (above the mean); influential genes labeled “H–L” have a strong positive correlation with pH (above the mean) and are linked to genes having a strong negative correlation with pH (below the mean); influential genes labeled “L–H” have a strong negative correlation with pH (below the mean) and are linked to genes having a strong positive correlation with pH (above the mean); influential genes labeled “L–L” have a strong negative correlation with pH (below the mean) and are linked to genes having a strong negative correlation with pH (below the mean). Genes in red are in cluster 4, the cluster that is the most correlated to pH.</p

Correspondence between clusters found by node clustering and bibliographic network.

<p>The list of genes for each cluster was submitted to IPA software and only one biological network was obtained. The eligible genes are those with a gene name accepted by IPA for having biological functions. An average of 83% of the eligible genes were included in the same network. IPA gives also the top biological functions associated with each cluster.</p

Radiatively Broadened Incandescent Sources

We study the incandescence of a semiconductor system characterized by a radiatively broadened material excitation. We show that the shape of the emission spectrum and the peak emissivity value are determined by the ratio between radiative and nonradiative relaxation rates of the material mode. Our system is a heavily doped quantum well, exhibiting a collective bright electronic excitation in the mid-infrared. The spontaneous emission rate of this collective mode strongly depends on the emission direction and, uncommonly for an intersubband system, can dominate nonradiative scattering processes. Consequently the incandescence spectrum undergoes strong modifications when the detection angle is varied. Incandescence is modeled solving quantum Langevin equations, including a microscopic description of the collective excitations, decaying into electronic and photonic baths. We demonstrate that the emissivity reaches unity value for a well-defined direction and presents an angular radiative pattern that is very different from that of an oscillating dipole