4.5. Data Analysis and Bioinformatics

Generated quantitative results were processed by UHR-IonStar for data formatting and cleanup, inter-group ratio calculation, and statistical testing by Student’s t-test. Optimal cutoffs for determining significantly changed proteins in each case-control pair were identified by an experimental null approach described previously [16]. Hierarchical clustering was performed by corresponding R packages. Gene Ontology (GO) analysis was performed by the Database for Annotation, Visualization, and Integrated Discovery (DAVID) Bioinformatics Resources v6.8 (http://david.abcc.ncifcrf.gov, accessed on 15 January 2021) [39]. Biological processes assigned by DAVID were manually curated and filtered. Pathway analysis was performed by Ingenuity Pathway Analysis (https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/, accessed on 15 January 2021) [40] and results were manually exported and compiled. Protein network analysis was performed by STRINGDB, and further processed and visualized by Cytoscape. All data visualization was done by ggplot2 package in R and Graphpad Prism.