Preparing Datasets for Comparative Analysis

Datasets used in Figure 1 were either obtained directly from authors (VAST⁴⁴ (link) and Cyclists⁴³ (link) datasets) or downloaded from publications⁴² (link) (SISA dataset) and R packages (Zeller dataset from the MetagenomicData⁴⁶ (link) and LIHC from the GSEABenchmarkeR⁴⁷ (link)) with help from the authors. The SISA dataset contains data from 543 individuals hospitalized due to arboviral infection with dengue, chikungunya, or Zika virus from a surveillance study in Ecuador collected from 2013 to 2017. In the SISA dataset we excluded columns with high level of missing values (pregnancy, “WomPreg,” and complete blood count test, which was not performed for all donors and includes the columns “PLT_count,” “Lymphocytes,” “CBC_N%,” “WBC_calc,” and “CBC_HCT”). In addition, nine donors with missing values were removed. The final SISA dataset after removal of columns and rows with missing values is available as Table S2. The Cyclists dataset contains data from the immune responses of 120 elderly individuals with a high-level of physical activity, i.e., master cyclists, and 75 age-matched controls with a low level of physical activity (non-cyclists) analyzed using flow cytometry (Table S4). The VAST dataset contains data from 72 individuals enrolled in the clinical study to evaluate humoral responses in a typhoid vaccine efficacy trial in a controlled human infection model. Only day 0 (day of the challenge) log-transformed data were used and are available for download as Table S5. Individuals were vaccinated with either a purified Vi-PS vaccine (35 individuals) or the Vi-TT vaccine (37 individuals) 1 month prior to oral challenge with live Salmonella Typhi. Of 72 individuals, 26 developed an acute typhoid infection following challenge. The Zeller dataset contains information on the microbiome species abundance in healthy individuals and colorectal cancer patients (Table S8). The data were accessed through the MetagenomicData package. In total 184 individuals were included, of which 93 were healthy controls and 91 colorectal cancer patients. The LIHC dataset obtained from the GSEABenchmarkeR package contains RNA expression data from 374 LIHC cells and 50 adjacent normal cells (Table S9).