Fig. 3: Identification of hub proteins in modules associated with HIV.

A–AA Scatter plots showing correlation of absolute effect sizes of protein-HIV significance (y-axis) and intra-modular connectivity (x-axis) among modules significantly associated with HIV. Positive correlations were observed in 15 protein modules while PM39 displayed a negative correlation. Modules PM1, PM5, PM6, PM10, PM14, PM17, PM25, PM26, PM30, PM31 and PM34 did not show significant correlations. Correlation coefficients (R) with their corresponding significance are shown where p < 0.05 were considered significant. The blue regression line shows this relationship while the error bands represent the 95% confidence interval for the regression line. Hub proteins are highlighted by red dots and labelled accordingly. Box plots show the expression levels of hub proteins by HIV status (children with HIV, n = 79; children without HIV, n = 610). Data are presented as median values with interquartile ranges (IQR). A two-sided t-test was used to compare expression levels, with Bonferroni-adjusted p < 0.05 considered statistically significant. Box plots indicate; median (middle line); 25th (first quartile, Q1) and 75th (third quartile, Q3) percentile (box limits); error bars (whiskers) represent 1.5*Q1 and Q3 while single points outside the error bars represent outliers. Abbreviations: PM, protein module; ∣β-coefficient∣, absolute beta coefficient estimate of a relationship between proteins in a module and HIV – the protein-HIV significance; R, correlation coefficient; p, p-value.