Fig. 1.

VDR is predicted as a key TF in AM and COPD disease gene. a, schematic diagram depicting systems biology approaches to identify the key TFs in tissue-resident macrophages and COPD-disease genes in AM. MRA: master regulatory analysis; PPI: protein-protein interaction; SG: signature genes. b, top-ranked key TFs for each of the seven tissue macrophages and for all seven tissue macrophages. #SG, number of signature genes; AM, alveolar macrophages; RPM, red pulp macrophages; PCM, peritoneal cavity macrophages; SIM, small intestine macrophages; BMM, bone marrow macrophages; ATM, adipose tissue macrophages; Common to Mϕ, common TF for all seven types of tissue macrophages. c, Comparison of the transcript levels of Vdr, Spic, Gata6 and Foxm1 in freshly purified AM, RPM, PCM, BMM, B cells (B) and CD8⁺ T cells (CD8) by qPCR. Data were average of 3 biological replicates per group. d, Comparison of the precision rates of community algorithm versus other algorithms for identifying COPD-disease genes. e, Top ranked key COPD-disease genes in AM. Shaded ones are known COPD disease genes and the others are newly identified in this study. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)