| Autor: |
A-Reum Nam, Kang-Hoon Lee, Hyeon-Ji Hwang, Schabort, Johannes J., An, Jae-Hoon, Won, Sung-Ho, Cho, Je-Yoel |
| Rok vydání: |
2020 |
| DOI: |
10.6084/m9.figshare.12687106.v1 |
| Popis: |
Additional file 1: Supplementary Figures. Figure S1. Data Quality Check for MBD sequencing. A) Saturation analysis for MBD-seq data from each sample was done using the MEDIPS package. Shown is the saturation analysis result derived from 22 MBD-sequencing samples. B) Coverage pattern analysis illustrates the fraction of CpGs covered by the given reads according to read depth. C) Pearson’s correlation for all counted peaks between experimental samples. Figure S2. Overview of DNA methylation peaks across samples throughout the full genome. IGV shows MBD-peaks (dark brown for 11 adjacent normal samples, dark blue for 11 cancer samples and input (gray) across the dog genome (Chr 1-38 and X). Differentially methylated bins (yellow), CpG islands (red) and gene annotations of CanFam3.1 (blue) are also displayed. Most of the peaks are well-enriched around CpG islands and genes and all experimental sets are performed with high similarity to each other. Figure S3. The expression level of the top 4 orthologous genes ranked by OncoScore in canine mammary tumor. Box plots show the expression level of four genes (TP63, LIFR, FOLH1 and WT1) in adjacent normal (n=8) and paired CMT tissues (n=8). Expression values are presented as FPKM calculated from RNA-sequencing data. Statistical p-value was calculated by Wilcoxon’s test. Figure S4. Adjustment of thresholds to select distinguished CMT-DMRs for intronic motif analysis. A) P-values for each DMR was extracted using a serial cutoff manner (upper 1~20%), B) Dendrogram for 22 cancer and adjacent normal tissue samples separate cancer groups from normal when CMT-DMRs are identified at the 10% cutoff in linear mixed model (LMM). Figure S5. Kaplan-Meier plots showed PAX5 and PAX6 expression’s reverse effect on the survival rate of breast cancer patients. Survival rates depend on A) PAX5 and B) PAX6 expression. Web-based KM-plotter ( https://kmplot.com/analysis/index.php?p=service ) was used for drawing KM plots. Figure S6. Validation of individual CG methylation around PAX5 motif regions in CDH5 and LRIG1 genes. Paired t-test for individual CG in A) CDH5 and B) LRIG1 intronic PAX5 motif region. Percentage of methylated cytosine (C (%)) is represented by (C/C+T) * 100. Red lines between CMT and adjacent normal indicate hypermethylation, while blue lines indicate hypomethylation (N: adjacent normal, C: CMT). Statistical p-value was calculated by paired t-test. |
| Databáze: |
OpenAIRE |
| Externí odkaz: |
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