Computational protocol: Acute Zika Virus Infection in an Endemic Area Shows Modest Proinflammatory Systemic Immunoactivation and Cytokine-Symptom Associations

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Protocol publication

[…] Differences in log2 cytokine levels between ZIKV-infected subjects and healthy controls were assessed using limma () with a significance level of p < 0.05 and a fold-change >2. Additionally, we used Mann–Whitney non-parametric analysis and rank product analysis () to compare the levels of plasma cytokines between ZIKV-infected subjects and healthy controls, and Chi-square tests to compare the detection frequency of each cytokine in ZIKV-infected subjects and healthy controls. The Spearman correlation test (p < 0.05 and R > 0.5) was used to identify associations between different cytokines/chemokines. To identify associations between cytokine levels and symptoms, we used Student’s t-test (p-value <0.05 and fold-change >2) to compare infected patients with and without specific symptoms. Random Forest analysis () was utilized to classify the importance of cytokines in predicting ZIKV infection and clinical symptoms (R package “randomForest”). The Wilcoxon matched-pair test was used to compare cytokine plasma levels in the same subjects in the acute and recovery phases (p-value < 0.05). We used GraphPad Prism 6.0 software (GraphPad Software, San Diego, CA, USA), R packages “heatmap2,” “corrplot,” and “ggplot” and Cytoscape to display the results. […]

Pipeline specifications

Software tools limma, randomforest, corrplot
Applications Miscellaneous, Gene expression microarray analysis
Organisms Zika virus, Homo sapiens, Human poliovirus 1 Mahoney