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. 2019 Apr;29(4):697–709. doi: 10.1101/gr.240093.118

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© 2019 Benayoun et al.; Published by Cold Spring Harbor Laboratory Press

This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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Figure 4. — Misregulated pathways during aging reveal the activation of an inflammatory innate immune signature. (A,B) Venn diagram for the overlap of significantly up-regulated (A) or down-regulated (B) genes with aging in each tissue called by DESeq2 1.6.3 at FDR < 5%. (C–F) Functional pathway enrichments (C,E–G) and transcription factor (TF) target enrichments (D) using the minimum hypergeometric test for differential RNA expression (C,D), H3K4me3 intensity (E), H3K4me3 breadth (F), and H3K27ac intensity (all enhancers) (G). Enriched pathways were plotted if four out of the six tests (RNA) or three out of the five tests (chromatin marks) were significant (FDR < 5%). (H) Heat maps of expression for all repetitive elements with significant differential expression with aging (TEtranscripts quantification and DESeq2 1.16.1 statistical test at FDR < 5%). Analysis of repetitive elements using HOMER, and overlap with TEtranscripts, is reported in Supplemental Table S6A–E.