Figure 4.

Differences in gene expression at homeostasis between the compartments. Microarrays were analysed using the Partek software. (A) Genes DR with a p adj. value < 0.01 and fold change > 2 or <-2 between the 3 types of macrophages at homeostasis (0h) were combined into a VENN graph. AM and MDM have 3,058 DR genes (green circle), AM and BMDM have 3,322 DR genes (red circle). There are 2,709 genes in common between the two lists. BMDM and MDM (blue circle) have only 144 genes DR, highlighting the closeness between these two types of derived-macrophages. (B) We ran a 2-way ANOVA test including the 2 variables: time-point and cell compartment). Genes that are the most differentially expressed between AM and MDM/BMDM (red, green and blue respectively) at 0 h were selected (p adj. value < 0.01 and fold change > 30 or <-30). The blue colour in the heat-map represents down-regulation of the gene and the red up-regulation of the gene in function to the average expression of the probeset. AM were found to express more VEGFA and its receptor FLT1, IDO1 and IL1B. BMDM and MDM expressed more genes related to adherence like integrin alpha 6 (ITGA6) and cell adhesion molecule 1 (CADM1). This result concurs with the different clusters found with Biolayout. Cluster 14 (C) includes genes highly expressed in MDM and BMDM such as ACE, where cluster 02 (D) is made of genes mostly expressed in AM.

Kapetanovic et al. BMC Genomics 2013 14:581   doi:10.1186/1471-2164-14-581
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