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. 2024 Jun;34(6):967–978. doi: 10.1101/gr.278637.123

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© 2024 Lee et al.; Published by Cold Spring Harbor Laboratory Press

This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.

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Figure 2. — Pan-metagenomics association studies (Pan-MGAS) of 43 cohorts from 23 different diseases and 14 countries (n = 2185). (A) We identified significantly enriched (top) and depleted (bottom) species of cohorts based on the effect sizes (ESs) of Wilcoxon rank-sum one-sided tests (ES ≥ 0.3; i.e., each dot represents the ES of an MSP in each disease data set); the complete list of values is provided in Supplemental Table S5. The blue dotted line indicates ES = 0.3; the red dotted line indicates ES = 0.5; and each dot in the plot represents one MSP within one disease cohort. (B) Scatter plots of the frequency of the significantly enriched/depleted cohorts of all MSPs (ES > 0.3): Each point represents an MSP; all values in the plot are integers; and jitter was added to remove overlapping points. The y-axis displays the total frequency of enriched/depleted cohorts (number of enriched cohorts + number of depleted cohorts), and the x-axis displays the subtracted frequency between enriched cohorts and depleted cohorts (number of enriched cohorts − number of depleted cohorts). Point coloring is based on the number of different diseases for which an MSP had an ES above 0.3. Commonly enriched/depleted species among cohorts were identified when total frequency ≥ 3 and absolute subtracted frequency ≥ 2. (C) Species found depleted (Anaerostipes hadrus) and enriched (Fusobacterium nucleatum subsp. animalis) in most disease cohorts. The blue dotted line indicates ES = 0.3; the red dotted line indicates ES = 0.5; and each dot in the plot represents one MSP within one disease cohort. Acronyms are as follows: (ACVD) acute coronary cardiovascular disease, (Ob) obesity, (CRC) colorectal cancer, (NSCLC) non-small-cell lung cancer, (RCC) renal cell carcinoma, (GDM) gestational diabetes mellitus, (T1D) type 1 diabetes, (T2D) type 2 diabetes, (LC) liver cirrhosis, (NAFLD) nonalcoholic fatty acid liver, (UC) ulcerative colitis, (CD) Crohn's disease, (BD) Behçet's disease, (RA) rheumatoid arthritis, (SPA) ankylosing spondylitis, (ME/CFS) myalgic encephalomyelitis/chronic fatigue syndrome, and (PD) Parkinson's disease.