MOESM1 of Transcriptomic analysis of monocytes from HIV-positive men on antiretroviral therapy reveals effects of tobacco smoking on interferon and stress response systems associated with depressive symptoms

David Lorenz, Vikas Misra, Dana Gabuzda
2019 Figshare  
Additional file 1: Figure S1. Overview and comparison of differentially expressed gene sets. (a) Number of differentially expressed genes from models contrasting HIV+ smokers vs. HIV- and HIV+ non-smokers and Venn diagrams of overlapping up- and down-regulated gene sets; (b) Number of differentially expressed genes from models contrasting HIV+ smokers vs. HIV- and HIV+ non-smokers in sensitivity analyses excluding HIV+ participants with HIV viral load > 200 and Venn diagrams of overlapping up-
more » ... of overlapping up- and down-regulated gene sets; (c) Venn diagrams comparing sets of up- and down-regulated genes in full cohort analyses vs. HIV viral load > 200 excluded cohort, with arrays from HIV- non-smokers as the reference; and (d) Venn diagrams comparing sets of up- and down-regulated genes in full cohort analyses vs. HIV viral load > 200 excluded cohort, with HIV+ nonsmokers as the reference. Genes with FDR-adjusted p value < 0.15, absolute log2 FC > 0.25 were deemed differentially expressed for all comparisons. Figure S2. Expression levels of genes associated with increased depressive symptoms stratified by HIV status, tobacco smoking, and CES-D score ≥ 16. Boxplots of normalized expression levels for genes associated with CES-D ≥ 16 in multivariate logistic regression models (Table 2). Values from five HIV- participants with CES-D ≥ 16 were excluded from plots for clarity. Horizontal bars denote medians, boxes span IQRs, whiskers extend to 1.5 x IQR. Dots denote expression values from individual arrays. Groups were compared using the Wilcoxon rank-sum test. Abbreviations: CES-D, Center for Epidemiological Studies Depression Scale; CES-D–, CES-D score < 16; CES-D16+, CES-D score ≥ 16; IQR, interquartile range; TS+, tobacco smoker; TS-, non-smoker. Figure S3. Expression levels of selected immune/interferon response, stress/chemical response, mitochondrion, and smoking-associated genes stratified by HIV status and marijuana or tobacco smoking. Boxplots of normalized gene expression levels for selected genes in Figur [...]
doi:10.6084/m9.figshare.11297015 fatcat:24ouczdjgjcinoo6mgf7tfrx3e