Skip to main content
. 2017 Nov 9;6:e31126. doi: 10.7554/eLife.31126

Figure 4. Gene expression signatures of inflammation.

Figure 4.

(a) Distributions of values for glia and for each Luminex variable marking inflammation, separated by brain region (labeling as in Figure 2A). (B) Correlation between gene metrics of inflammation (x-axis) and protein metrics of inflammation (y-axis) in each brain region. Gene signatures are defined as the module eigengene (ME) of the module with the largest enrichment for the GO term ‘inflammatory response’, and protein metrics are the truncated quantifications of the Luminex protein most highly correlated with each ME. (C) Gene (lower left) and protein (upper right) expression markers of inflammation are highly correlated between brain regions. Dots represent donors with x- and y-axes corresponding to the gene and protein values in B. Pairwise brain region correlations are shown below in each box. Blue circle and orange box correspond to donors in D. (D) IHC for IBA1 in a donor showing inflammation across regions (left, orange), and in a donor showing higher levels of inflammatory marker genes in hippocampus than cortex (right; blue). See also Figure 4—source datas 1–3.

Figure 4—source data 1. Module assignments and associated module eigengene correlations for each gene in the four regional WGCNA networks.
elife-31126-fig4-data1.xlsx (2.1MB, xlsx)
DOI: 10.7554/eLife.31126.015
Figure 4—source data 2. Module annotation for cell types.
Cell type gene lists are derived from Zhang et al. (2014) and NeuroExpresso in the left and right panels, respectively, and enrichment p-values for each module are calculated using a hypergeometric test and are Bonferroni-corrected.
elife-31126-fig4-data2.xlsx (52.6KB, xlsx)
DOI: 10.7554/eLife.31126.016
Figure 4—source data 3. Module comparison with demographic and pathology metrics.
Module eigengene expression is compared with 24 demographic and pathology metrics (including Dementia/control, AD/control, sex, measures of tau and abeta pathology, and inflammatory markers) using SVA, and p-values are Bonferroni-corrected.
elife-31126-fig4-data3.xlsx (51.2KB, xlsx)
DOI: 10.7554/eLife.31126.017