Figure 3
Gene clustering of brain activity-dependent genes reveals a reciprocal loss of neuronal genes inversely proportional to a rise in glial genes. (A) Analysis of the expression of 1998 activity-dependent genes (|FC|≥ 1.3, FDR ≤ 1%) as a function of the simulated PMI revealed two significant clusters of 1427 of the genes (p < 0.001, r > 0.95, n = 7). AlegroMcode software predicted the presence of two kernels, one containing 474 genes expressed by glia represented in red and another of 317 genes predicted to be expressed by neurons. No differentiation between astroglia and microglia could be made in the glial gene cluster. Each node (circle) represents a gene and the links between nodes represents a significant correlation. The thickness and length of each link is proportional to the correlation value. (B) While neuronal gene expression decreased as function of time, glial gene expression increased. Stable genes are composed of 6754 genes that did not show any significant increase or decrease of expression during the simulated PMI. The majority (between 75 and 89%) of commonly used housekeeping genes are stable until 12 H then showed an increase of variability at the 24 H time point. Error bars on glial and neuronal cells correspond to the weighted standard error of the mean. The error bar for the stable and housekeeping genes corresponds to the standard deviation. Gene expression values are normalized to expression at time 0. (C) The 500 activity-dependent genes that were most downregulated in healthy post-mortem brain were used to separate the 7 time points of the simulated PMI by PCA. The first component projection of the PCA has a value of 55%, its projection on the x-axis show a separation of the time points in order of 0H, 2H, 1H, 8H, 4H, 12H and 24H. No other meaningful separation was found on other components. (D) The quality of the RNA, assessed by the commonly used RIN number and gel electrophoresis, showed no clear signs of degradation (Supplementary_Material_S1).
