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.