Expression profilings of 39 genes selected by ANOVA could separate precursors of murine dendritic cells and macrophages

Abstract

Dendritic cells (DCs) and macrophages share some stages in the development and function of antigen presentation. But it is difficult to separate them from their precursors. We used one-way ANOVA (analysis of variances) on murine expression profilings of several hematopoietic cells associated with DCs and macrophages to find the genes with great differences across the cell groups. These groups were the DCs from spleen, cultivated DCs, DC precursors, DC progenitors, DC progenitor cell lines, hematopoietic stem cell (HSC), and bone marrow-derived macrophages. The data of expression profilings were all downloaded from GEO and ArrayExpress database. After the normalization of 11 housekeeping genes across 42 arrays, we got 39 genes (44 probesets) by analysis of one-way ANOVA (Bonferroni step-down) with p values cutoff of 0.05. These genes (probesets) could separate the hematopoietic cells well by the methods of unsupervised hierarchical clustering and principal component analysis (PCA). The class prediction also indicated that these genes could separate the precursors of DC and macrophages with 20 arrays composed of 5 cell types with the same normalization. The accuracy rate of class prediction was 90% (18/20). The genes selected by one-way ANOVA included those of MHC (major histocompatibility complex) and defense of immunity, cell adhesion, chemokine or its receptors, and transcription factors. The results indicated that these 39 genes could separate precursors of DC and macrophages very clearly. It was suggested that these genes might represent some important molecules that related with the precursors of DCs and macrophages, and were worthy for further study.