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. 2019 Nov 27;10:1229. doi: 10.3389/fgene.2019.01229

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Copyright © 2019 Declerck and Vanden Berghe

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Weighted Correlation Network Analysis (WGCNA) consensus module is influenced by underlying immune cell type composition and immune cell infiltration. (A) Blood immune cell type (B-cells, NK-cells, CD4+ T-cells, CD8+ T-cells, granulocytes, and monocytes) composition shift in atherosclerosis (blue) and Alzheimer’s disease (AD) (green) patients compared to controls estimated by the method of Houseman. Error bars represent 95% confidence intervals. (B) Estimated cell type composition in healthy aorta, aorta atherosclerotic plaque (ao_plaque), and carotid plaque (car_plaque). Relative cell type composition was estimated using reference methylomes of aortic smooth muscle cells (AoSMC), endothelial cells (HUVEC), fibroblasts (ProgFib), and immune cells (IC) (see Methods for more details). (C) Correlation between estimated IC infiltration and the eigengenes of the WGCNA consensus module (ME21) in aorta and carotid plaques. A negative correlation was found between estimated IC infiltration and ME21 eigengenes, which corresponds with the negative association found between module ME21 eigengenes and methylation in AD and atherosclerosis (i.e., AD and atherosclerosis patients have lower ME21 eigengenes compared to controls).