Inter-individual differences between pigs. The mean expression of the probesets in AM, BMDM and MDM combined, +/- LPS, of the 25 pigs were analysed. Two striking examples are the SLA-6 (A) and CNNM3 (B) genes. In one Landrace pig (pig number 3) the expression value of SLA-6 is significantly lower than the others. For the gene CNNM3, two Piétrain pigs (pigs 13 and 14) have a lower expression compared to the others pigs. These differences suggest a natural null-mutation of the genes. Number of probesets in function of their variance are graph for cells at 0 h (C) and 7 h (D) For each type of cell (MDM in blue, BMDM in red and AM in green), the average expression of each probesets has been calculated with its SED. Percentage of variance (SED/Average*100), rounded-up to a whole number, was plotted. Most of the probesets have a % of variance <10. We were interested in the list of probesets having a high variability between pigs (>20%). (E) We analysed this list of probesets for each type of cell and timing with the DAVID algorithm (http://david.abcc.ncifcrf.gov webcite) in order to cluster them in function of their biological process (lowest clustering option), using the list of expressed gene as background. The red dashed line represents the usual enrichment score threshold (1.3). A score > 1.3 is definitively playing an important role. In each case, the cluster of “immune response” was over this threshold.
Kapetanovic et al. BMC Genomics 2013 14:581 doi:10.1186/1471-2164-14-581