Additional file 2 of A reciprocal relationship between markers of genomic DNA damage and alpha-synuclein pathology in dementia with Lewy bodies

Supplementary Material 2. Supplementary table 2. Proteomic detection list and abundance analysis. Proteins identified as per the UniProt database and subsequently confirmed to be present with >2 unique peptides as well as being detected in >70% of samples are listed. For each protein, Entrez gene ID, gene name, individual Z-scores within batches (B1-3) for each sample are provided as well as pooled difference (DLB-Con), -Log(p-value) and significance (FDR<0.1). + = significant. Supplementary table 3. DAVID UniProt Keywords. Significantly enriched clusters from DAVID uniport keywords analysis. Enrichment database category, Keyword number, Keyword term, number of proteins present in upregulated list (count), % coverage of enrichment term, p value, associated genes and protein names are provided. Additionally detected term associated proteins within the background reference list (List Total), total proteins associated with the term (Pop Total), the fold enrichment, FDR adjustment and-Log10FDR values are provided. Supplementary table 4. DAVID GO Terms. Significantly enriched clusters from David GO terms analysis. Enrichment database category, Go number, term name, number of proteins present in upregulated list (count), % coverage of enrichment term, p value, associated genes and protein names are provided. Additionally detected term associated proteins within the background reference list (List Total), total proteins associated with the term (Pop Total), the fold enrichment, FDR adjustment and -Log10FDR values are provided. Supplementary table 5. STRING database GO term analysis of Cellular response to DNA damaging stimulus. All GO terms mapped to those proteins significantly upregulated which are associated with cellular response to DNA damaging stimulus. term ID, description, those upregulated proteins associated with the term (observed gene count), those present in the background list (Background gene count), strength of enrichment, FDR and matching protein ID and names are provided. Supplementary table 6. STRING database identified proteins and their associated DNA damage repair function. Identified proteins are listed with Gene symbol, Entrez gene ID, Gene names, an indication of their involvement in DNA damage repair pathways, a suggested DDR function and supportive citations. For DDR pathways, base-excision repair (BER), Double strand break repair (DSB), Non-homologous end joining (NHEJ) and homologous recombination (HR) as well as general role in repair is provided.

补充材料2. 补充表2. 蛋白质组学检测列表与丰度分析
根据UniProt数据库鉴定，并经确认存在>2个独特肽段且在>70%样本中被检测到的蛋白质均已列出。针对每个蛋白质，提供了Entrez基因ID、基因名称、各样本在批次（B1-3）内的个体Z值，以及合并差异（DLB-Con）、-Log(p值)和显著性（FDR<0.1）。+表示显著。
补充表3. DAVID UniProt关键词
DAVID UniProt关键词分析中显著富集的聚类。提供了富集数据库类别、关键词编号、关键词术语、上调列表中的蛋白质数量（计数）、富集术语的覆盖率百分比、p值、相关基因及蛋白质名称。此外，还提供了背景参考列表中检测到的术语相关蛋白质（列表总数）、与该术语相关的总蛋白质数（群体总数）、富集倍数、FDR校正及-Log10(FDR)值。
补充表4. DAVID基因本体术语
DAVID基因本体术语分析中显著富集的聚类。提供了富集数据库类别、基因本体术语编号、术语名称、上调列表中的蛋白质数量（计数）、富集术语的覆盖率百分比、p值、相关基因及蛋白质名称。此外，还提供了背景参考列表中检测到的术语相关蛋白质（列表总数）、与该术语相关的总蛋白质数（群体总数）、富集倍数、FDR校正及-Log10(FDR)值。
补充表5. STRING数据库中细胞对DNA损伤刺激应答的基因本体术语分析
所有映射到与细胞对DNA损伤刺激应答相关的显著上调蛋白质的基因本体术语均已列出。提供了术语ID、描述、与该术语相关的上调蛋白质（观察到的基因数）、背景列表中的蛋白质（背景基因数）、富集强度、FDR及匹配的蛋白质ID和名称。
补充表6. STRING数据库鉴定的蛋白质及其相关DNA损伤修复功能
列出的鉴定蛋白质包含基因符号、Entrez基因ID、基因名称、参与DNA损伤修复通路的指示、建议的DNA损伤修复功能及支持性文献引用。针对DNA损伤修复通路，提供了碱基切除修复（BER）、双链断裂修复（DSB）、非同源末端连接（NHEJ）、同源重组（HR）以及修复中的一般作用。