The CSF-1R pTyr721-regulated macrophage transcriptome. (A) Schematic depiction of the CSF-1Rs in the macrophage cell lines used to assess the necessity (loss of function, upper panels) and sufficiency (gain of function, lower panels) of pTyr-721 signaling in macrophages. The CSF-1R domains (extracellular [ECD]; transmembrane [TM], and tyrosine kinase [TK]) and the intracellular CSF-1R Tyr (Y, black) residues mutated to Phe (F, red) are indicated. (B) Pairwise comparisons of gene expression data for all 28 361 transcripts detected on microarrays, showing high Pearson correlation coefficients between biological replicates and the expected hierarchical clustering of samples, as a function of genotype and CSF-1 treatment. Results for M−/−.WT and M−/−.Y721F (upper panel) and M−/−.3ABY721 and M−/−.3AB (lower panel) are shown as heat maps illustrating the significant differences in gene expression between Tyr-721–expressing and Tyr-721–nonexpressing cells, each with an associated color key and histogram (−, without CSF-1; +, with 120 ng/mL of CSF-1; biological replicates are indicated by the numerals 1 and 2). (C-E) Venn diagrams, representing the size of the pTyr-721–regulated transcriptome, identified by each approach. To obtain the pTyr-721–regulated genes, the CSF-1–regulated transcripts expressed in either M−/−.WT or M−/−.3ABY721 cells were compared with those of the corresponding Y721F mutant cells. (C) The Y721F mutation (1904 CSF-1–regulated mRNAs) reduced the number of CSF-1–regulated mRNAs of M−/−.WT macrophages (2174) by 270 transcripts. However, of the CSF-1–regulated genes in both cell types, 1713 (∼9% of 19 000 total mouse genes) were differentially regulated in both data sets. (D) The addition of CSF1R Y721 to the 3AB background increased the number of CSF-1–regulated transcripts by 250 (from 870 to 1120). Of the CSF-1–regulated genes in both cell types, 244 (∼1.3% of 19 000 total mouse genes) were differentially regulated in both data sets. (E) Only 34 genes are common between the 2 datasets.