Figure 3

Clusters of pig macrophage gene expression using Biolayout. 3D visualization of a Pearson correlation (R=0.91) from the analysis of the 140 pigs micro-arrays (BMDM, MDM and AM - at 2 timepoint 0 h and 7 h). Each sphere represents an individual probeset and is composed of 5203 nodes and 29799 edges. In order to more easily differentiate the data from background noise, probesets with an expression intensity <50 in all samples have been removed from the analysis. Clustering of the graph, using the MCL algorithm (MCL = 2.2), gave a total of 505 clusters, all listed in Additional file 4. (A-F) To identify the different superclusters, histograms of some clusters have been included in the figure showing the average expression of genes on all condition (MDM 0 h, MDM 7 h, BMDM 0 h, BMDM 7 h, AM 0 h, AM 7 h). In these histogram plots for every condition the data for each breed are shown in the same order (LR-LW-DU-PIE-HAM). Cells treated with LPS are highlighted in orange in each graph.