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Supplementary Figures – Methylome of Skeletal Muscle Tissue in Patients with Hypertension and Diabetes Undergoing Cardiopulmonary Bypass

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posted on 22.11.2021, 09:59 by Figshare Future Science GroupFigshare Future Science Group, Ghazal Aghagoli, Andrew Del Re, Naohiro Yano, Zhiqi Zhang, Ahmad Aboul Gheit, Ronald K. Phillips, Frank W. Sellke, Alexey V. Fedulov

Supplementary Figure 1. Normalized samples m-value box and whiskers chart

Average m-values across the entire sample were plotted as box and whiskers. The middle line is the median, box represents the upper and the lower quartile, while the whiskers correspond to the 90th and 10th percentile of the data.

Supplementary Figure 2. Histograms of beta values and m-values

Each sample is a line, beta-values (or M-values) are on the horizontal axis and their frequencies on the vertical axis. Two peaks correspond to two probe types (I and II) present on the MethylationEPIC array. Sample colors correspond to a categorical attribute. A: beta-values, and B: m-values for pre-operative samples only; C, D: beta and M-values for all samples.

Supplementary Figure 3. Venn diagram illustrating ANOA results.

A). Number of DMRs in each contrast and pairwise overlap (in percent) between contrasts. B). Four key contrasts queried for overlapping probes at the same time.

Supplementary Figure 4. Direct Interactions network

A list of differentially methylated loci is loaded into a network analysis software package (Metacore) which determines all known direct interactions between all factors from the list based on its database of biochemical interactions and designs a network figure.

Network analysis of Control vs. Hypertension + Uncontrolled Diabetes list shows that the gene names associated with the altered loci form a tightly interacting network with 560 hubs and 7055 edges. The network was designed using ‘direct interactions’ algorithm, meaning only the gene names from the list are included. The factors (genes) are positioned based on their cellular localization (top to bottom: Extracellular, Membrane, Cytoplasm, Nucleus, Unspecified). Each factor is depicted by a symbol (varies with a biological nature of the factor) and each known interaction is shown by a

connecting line. The contrast intentionally emphasizes the interaction lines and not the factor symbols and serves to illustrate the density of interactions. A.) Actual data. B.) Control list of the same number of random genes.

Supplementary Figure 5. Top-50 pathways

Names and p-values for top 50 pathways involved (A-C) and top 50 GoProcesses list (D-E).

Supplementary Figure 6. Top 50 pathway maps

Names and p-values for top 50 pathway maps enriched with DMLs found in comparing pre- vs. postoperative samples (n=941).

Funding

the Qinghai Province Application of Basic Research Projects grants (number 2019-SF-135 and number 2021-ZJ-756) awarded to Prof. Aiqin Zhu.

the National Natural Science Foundation of China grants (No. 82001129) awarded to Dr. Jie Meng

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