Additional file 1 of DNA methylation patterns associated with konzo in Sub-Saharan Africa

Additional file 1: Table S1. Sample collection information. Sample IDs were relabeled with "Analysis ID" for improved readability on figures. Cohort specific information, location of sample collection, and age are also provided (average age = 13 years old). Table S2. Beta values of all konzo case and control samples. Beta values for individual konzo samples are labeled columns K1–K16; beta values for individual control samples are labeled C1–C16. Averages for both groups are labeled Average_Konzo_Bvalue and Average_Contrl_Bvalue. Mean for each group is labeled Average_Konzo_Bvalue_Total and Average_Contrl_Bvalue_Total. Table S3. DNA Methylation analysis tools, functions and references. Table S4. Output significantly differentially methylated probes from bioinformatic analysis. Threshold for significance: FDR p value < 0.05, log2 fold-change of less than or equal to − 1 or greater than or equal to 1. Column headers include the Illumina ID (IlmnID), Chromosome Number (Chromosome) and location (Coordinate_start or Coordinate_end), positive or negative strand (Strand), gene name (Name), location of probe to CpG (Group), log2 fold-change value (logFC), and FDR adjusted p value (adj.P.Val). Table S5. Output significantly differentially methylated probes from bioinformatic analysis with immune cell fraction analysis. Threshold for significance: FDR p value < 0.05, log2 fold-change of less than or equal to − 1 or greater than or equal to 1. Column headers include the Illumina ID (IlmnID), Chromosome Number (Chromosome) and location (Coordinate_start or Coordinate_end), positive or negative strand (Strand), gene name (Name), location of probe to CpG (Group), log2 fold-change value (logFC), and FDR adjusted p value (adj.P.Val). Table S6. Cell-type fraction means for Konzo cases and controls. Standard deviation (sd) was calculated for each mean. Column headers include: cell type (CellType), cohort specifics (Condition), mean (Mean), standard deviation (sd), and Upper (mean + sd) and Lower (mean-sd) bounds. Table S7. Output significantly enriched GO Terms. Threshold for significance: p value < 0.05. Column headers include the GO ID (ID), GO Term Description (GO Description), absolute log10 p value (abs_log10_pval), log10 p value (log10_pval), p value (pval), and genes associated with GO ID (genes). Table S8. Targeted methylation analysis results. ProbeID: Illumina probe IDs; Genes: Associated genes; Transcripts: Associated transcripts; Chromosome: chromosomal position; Region: Regions in the chromosome that get affected; %MethylationDifference: Difference in methylation percentage; logFC: Difference in log (base 2) fold change; p value: associated p value.

附加文件1：表S1。样本采集信息。为提升图表可读性，样本编号已重新标注为“分析ID（Analysis ID）”。本表格同时提供队列特定信息、样本采集地点及年龄信息（平均年龄=13岁）。
表S2。所有Konzo病例及对照样本的β值。单例Konzo样本的β值以K1–K16作为列标签；单例对照样本的β值以C1–C16作为列标签。两组的平均值分别标注为Average_Konzo_Bvalue与Average_Contrl_Bvalue。每组的总均值分别标注为Average_Konzo_Bvalue_Total与Average_Contrl_Bvalue_Total。
表S3。DNA甲基化（DNA Methylation）分析工具、功能及参考文献。
表S4。生物信息学分析得到的显著差异甲基化探针结果。显著性阈值：假发现率（FDR）校正p值<0.05，log2倍数变化≤−1或≥1。列标题包括：Illumina ID（IlmnID）、染色体编号（Chromosome）及位置（Coordinate_start或Coordinate_end）、正负链（Strand）、基因名称（Name）、探针至CpG位点的位置（Group）、log2倍数变化值（logFC）及FDR校正p值（adj.P.Val）。
表S5。整合免疫细胞组分分析的生物信息学分析所得显著差异甲基化探针结果。显著性阈值：FDR校正p值<0.05，log2倍数变化≤−1或≥1。列标题包括：Illumina ID（IlmnID）、染色体编号（Chromosome）及位置（Coordinate_start或Coordinate_end）、正负链（Strand）、基因名称（Name）、探针至CpG位点的位置（Group）、log2倍数变化值（logFC）及FDR校正p值（adj.P.Val）。
表S6。Konzo病例与对照的细胞类型组分平均值。已为每个平均值计算标准差（sd）。列标题包括：细胞类型（CellType）、队列特定信息（Condition）、平均值（Mean）、标准差（sd）、上限（mean+sd）与下限（mean−sd）。
表S7。显著富集的基因本体（Gene Ontology, GO）术语结果。显著性阈值：p值<0.05。列标题包括：GO ID（ID）、GO术语描述（GO Description）、绝对log10 p值（abs_log10_pval）、log10 p值（log10_pval）、p值（pval）以及与该GO ID相关联的基因（genes）。
表S8。靶向甲基化分析结果。各字段说明如下：ProbeID：Illumina探针ID；Genes：关联基因；Transcripts：关联转录本；Chromosome：染色体位置；Region：受影响的染色体区域；%MethylationDifference：甲基化百分比差异；logFC：log2（以2为底）倍数变化值；p value：关联p值。