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Rheumatoid arthritis Rheumatoid arthritisRheumatoid arthritis is a chronic and inflammatory autoimmune disease that primarily affects joint health. It is one of the most prevalent inflammatory diseases and symptoms include swollen, tender, and stiff joints (Smolen JS et al. (2016)). As with other chronic autoimmune diseases, rheumatoid arthritis is heterogeneous and has a higher prevalence in females (Radu AF et al. (2021)). Risk factors include smoking, previous infections, and low socioeconomic status (Smolen JS et al. (2016)). Differential abundance and machine learning analysisThis section presents the disease-specific results of the differential abundance and machine learning analyses. The analyses are reported for three comparisons: 1) disease vs. all other diseases, 2) disease vs. diseases from the same class, and 3) disease vs. healthy samples. Disease vs All other
Disease vs Class
Disease vs Healthy
Figure 1: In the volcano plot, proteins are plotted based on their fold change (logFC) on the x-axis and the statistical significance of the change (-log10 adjusted p-value) on the y-axis. Proteins considered differentially abundant are highlighted, defined by an adjusted p-value < 0.05 and an absolute logFC > 0.5.
Figure 2: Summary of machine learning selected proteins. Reported is the average importance across all bootstraps and the standard deviation for the 10 most important proteins. Feature importance is the model estimates for each protein, normalized to a scale of 1-100. Table 1: The summary table lists the results for all comparisons, sorted by p-value by default. It includes key metrics such as fold change and adjusted p-value, to allow exploration of the most significant proteins for each comparison.
The table also shows the average protein importance across all bootstraps.
Figure 1: In the volcano plot, proteins are plotted based on their fold change (logFC) on the x-axis and the statistical significance of the change (-log10 adjusted p-value) on the y-axis. Proteins considered differentially abundant are highlighted, defined by an adjusted p-value < 0.05 and an absolute logFC > 0.5.
Figure 2: Summary of machine learning selected proteins. Reported is the average importance across all bootstraps and the standard deviation for the 10 most important proteins. Feature importance is the model estimates for each protein, normalized to a scale of 1-100. Table 1: The summary table lists the results for all comparisons, sorted by p-value by default. It includes key metrics such as fold change and adjusted p-value, to allow exploration of the most significant proteins for each comparison.
The table also shows the average protein importance across all bootstraps.
Figure 1: In the volcano plot, proteins are plotted based on their fold change (logFC) on the x-axis and the statistical significance of the change (-log10 adjusted p-value) on the y-axis. Proteins considered differentially abundant are highlighted, defined by an adjusted p-value < 0.05 and an absolute logFC > 0.5.
Figure 2: Summary of machine learning selected proteins. Reported is the average importance across all bootstraps and the standard deviation for the 10 most important proteins. Feature importance is the model estimates for each protein, normalized to a scale of 1-100. Table 1: The summary table lists the results for all comparisons, sorted by p-value by default. It includes key metrics such as fold change and adjusted p-value, to allow exploration of the most significant proteins for each comparison.
The table also shows the average protein importance across all bootstraps.
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The Human Protein Atlas
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