Syncytiotrophoblast Membrane Extracellular Vesicles (STB-EVs) Derived Proteomic Biomarkers of Preeclampsia-Supplemental Data
Description
The file contains the full list of differentially expressed proteins and results of functional enrichment analysis ( Gene Ontology; Biological Processes (GO:BP), Gene Ontology; Molecular Functions (GO:MF), Gene Ontology; Cellular Components (GO:CC) and KEGG Pathways) of placenta, medium/large syncytiotrophoblast membrane extracellular vesicles (m/lSTB-EVs) and small syncytiotrophoblast membrane extracellular vesicles (sSTB-EVs) in preeclampsia (PE) compared to normal (NP)
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Bioinformatic analysis of proteomic data from placenta tissue, medium/large and small STB-EVs Analysis was done in Perseus (Max Planck Institute of biochemistry) using the accompanying Perseus documentation and tutorials. We pre-processed the raw data by log transforming and filtering to remove invalid data. Missing values were randomly imputed from a normal distribution with the following settings: width = 0.3 and downshift = 1.8. The underlying distribution was inspected visually with a histogram before and after missing data imputation to ensure conformity to normal distribution. The data was further transforming by subtracting each (transformed) value from the highest occurring protein expression value. The data was further explored with principal component analysis (PCA), heatmap and Pearson correlation matrices. Correlation index and hierarchical clustering were performed on the data. Samples that clustered differently on the hierarchical map and PCA and had a Pearson correlation index less than 0.8 were considered outliers and excluded. Differential expression was performed by conducting a two-sample independent student t-test. Multiple testing was corrected via permutation-based FDR with the following settings and significance was set at less than 0.05. G: Profiler ([https://biit.cs.ut.ee/gprofiler/gost], RRID:SCR_006809) was used for functional enrichment analysis of the differentially expressed proteins (DEPs). The enriched pathways/terms from the KEGG database and Gene ontology database; gene ontology biological process (GO: BP), gene ontology molecular function (GO: MF), and gene ontology clinical component (GO: CC) were ascertained for each set of DEPs by applying hypergeometric testing and variance measured with standard error. Multiple testing was corrected by Benjamin Hochberg correction, and the significance level was set to < 0.05.