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Additional file 1: of Gene expression meta-analysis of Parkinson’s disease and its relationship with Alzheimer’s disease

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posted on 28.02.2019, 05:00 by Jack Kelly, Rana Moyeed, Camille Carroll, Diego Albani, Xinzhong Li
Table S1. Information about each study used in our meta-analysis after removal of outlier samples. Table S2. Differentially expressed genes identified in our meta-analysis that have been identified as PD risk genes in a recent GWAS meta-analysis [33]. Table S3. IPA canonical pathway analysis for significant pathways identified using all PD DEGs, included with the information for pathways shared with those identified as significant using all AD DEGs. Table S4. IPA canonical pathway analysis for significant pathways identified using down-regulated PD DEGs. Table S5. IPA upstream regulator analysis for up and down regulated PD DEGs analysed separately. Table S6. Top 10 hubs found in the protein-protein interaction network (PPIN) analysis subnetwork created using the top 30 PD DEGs. Table S7. The direction of differential expression between the common DEGs found between AD and PD. Figure S1. Selecting filtering threshold for microarray data. The percentage of studies called absent in a mas5 present absent call for each probe was calculated, and threshold determined by minimizing Anderson-Darling normality tests and giving optimal Q-Q plot of the Z-scores after meta-analysis. The Q-Q plot for (A) 5%, (B) 10%, (C) 15%, (D) 20% and (E) 30% filtering. After 15% filtering A-D p-values were minimized (F) and the 15% Q-Q plot gave closest values to normality. A-D is Anderson-Darling normality test. Figure S2. RNAseq data vs. microarray gene expression data. Average absolute expression level of RNA-seq log2(TPM) of SN tissue from GTEx database plotted against RMA normalised and filtered intensity of microarray control and PD data used in this meta-analysis. The Pearson correlation coefficient between the control microarray data and healthy RNA-seq data (A) is 0.70 (pvalue < 2.2e-16) showing that the expression values of genes between microarray and RNA-seq are correlated and expression data distribution is similar. The Pearson correlation between the healthy RNA-seq and PD microarray data (B) is actually higher than between RNA-seq and control microarray at 0.73 (pvalue < 2.2e-16), when it would be expected to be lower due to some genes being differentially expressed. When using only DEGs, correlation between healthy RNA-seq and control microarray (C) and PD microarray (D) data this difference in correlation is minimised to 0.65 (pvalue < 2.2e-16) and 0.66 (pvalue < 2.2e-16) respectively, suggesting that the difference in correlation could be due to the larger sample size of the PD data. (DOCX 1024 kb)

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