Cytokine ranking via mutual information algorithm correlates cytokine profiles with presenting disease severity in patients infected with SARS-CoV-2
- Brown Experimentalists Against COVID-19 (BEACON) Group, Brown University, United States
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, United States
- The Joint Program in Cancer Biology, Brown University and Lifespan Health System, United States
- Cancer Center at Brown University, Warren Alpert Medical School, Brown University, United States
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, United States
- Pathobiology Graduate Program, Warren Alpert Medical School, Brown University, United States
- Department of Molecular Microbiology and Immunology, Brown University, United States
- Department of Surgery, Lifespan Health System and Warren Alpert Medical School, Brown University, United States
- Biostatistics and Bioinformatics Facility, Fox Chase Cancer Center, Temple University Health System, United States
- Hematology-Oncology Division, Department of Medicine, Lifespan Health System and Warren Alpert Medical School, Brown University, United States
Figures
Figure 1
Mutual information COVID Severity Score (CSS) relevancy matrix.
(A) Comprehensive matrix of relevancy to CSS of all variables assessed by mutual information algorithm, relevancy scores computed for not-yet selected variables are shown in each column, and variables are ordered to place maximum local scores on the diagonal, yielding a list in decreasing order from the upper left of variable relevancy. Warmer colors indicate higher relevancy, while cooler colors indicate higher redundancy. (B) COVID Severity Score Table with breakdown of categories as well as sample size per category.
-
Figure 1—source data 1
Mutual algorithm criteria table.
- https://cdn.elifesciences.org/articles/64958/elife-64958-fig1-data1-v2.docx
Figure 2
Age, macrophage colony-stimulating factor (M-CSF), and chest x-ray are the most predictive variables for COVID Severity Score (CSS).
(A) The y-axis is CSS, and the x-axis is age in years with points colored by chest x-ray status. (B) The y-axis is M-CSF concentration in pg/mL, and the x-axis is age in years, with points colored based on CSS. See individual legends below graphs. (C) Receiver operating characteristic (ROC) curve predicting CSS 4–5 using age, M-CSF, IP-10, IL-18, and IL-1RA, and ROC curve predicting CSS 4–5 using only age.
-
Figure 2—source data 1
Patient information.
- https://cdn.elifesciences.org/articles/64958/elife-64958-fig2-data1-v2.docx
Figure 3
Violin plot representations of cytokine expression levels ordered by COVID Severity Score (CSS).
Cytokines ordered by row from upper left corner based on mutual information relevancy matrix (upper left being most relevant and lower right being least relevant). The x-axis is CSS, and the y-axis is analyte concentration in pg/mL. One-way ANOVA F values and p values are listed on each plot. Source code 1. R code with sections to apply the varrank package to the source data, create a receiver operating characteristic curve, and calculate analysis of variance for each cytokine.
-
Figure 3—source data 1
Raw data.
Source Data Table 1. Mutual algorithm criteria table. *Documented obesity or overweight for height < 99th percentile. Source Data Table 2. Patient information.
- https://cdn.elifesciences.org/articles/64958/elife-64958-fig3-data1-v2.zip
Author response image 1
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Biological samples (Human) | Human plasma | Lifespan Brown COVID-19 Biobank | See data table | 48 unique patients |
| Biological samples (Human) | Human plasma | Lee BioSolutions | 991–58-PS | 24 unique patients |
| Commercial assay or kit | MILLIPLEX MAP Human Immunology Multiplex Assay | Millipore Sigma | 15-Plex # HCYTA-60K | |
| Software, algorithm | R | R Project for Statistical Computing | RRID:SCR_001905 | |
| Other | Luminex 100/200 System assay platform | Thermo Fisher Scientific | https://www.luminexcorp.com/luminex-100200 |
Additional files
-
Source code 1
Cytokine Mutual Information R Script.
- https://cdn.elifesciences.org/articles/64958/elife-64958-code1-v2.zip
-
Transparent reporting form
- https://cdn.elifesciences.org/articles/64958/elife-64958-transrepform-v2.docx
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Cytokine ranking via mutual information algorithm correlates cytokine profiles with presenting disease severity in patients infected with SARS-CoV-2
eLife 10:e64958.
https://doi.org/10.7554/eLife.64958
