2.4. Protein–Protein Interaction Network Prediction

The www.string-db.org (version 11, accessed on 20 June 2020) webpage was navigated to analyze protein–protein interaction networks. STRiNG provides a database of known and predicted protein–protein interactions including indirect (functional) and direct (physical) associations arising from computational prediction, knowledge transferable and primary databases, such as participating in the same biological process or protein class (gene ontology). STRiNG (Search Tool for Retrieval of Interacting Genes/Proteins) can be searched by single or multiple protein names, or by amino acid sequences in any available formats. In this study, a total of 99 accession numbers derived from 54 and 45 increased and decreased abundant proteins was inserted as protein identifier. The multiple proteins input was selected. Then, the organism of interest (E. histolytica) was specified before clicking the SEARCH button. Then, the network was displayed to show the predicted network of association for a group of proteins. Proteins were represented by the nodes, and edges showed predicted functional associations. By clicking on a node gave several details of the protein and the edge displayed a detailed evidence breakdown. The line or edge could be seen in seven different colors, which represented different evidence used in protein relation prediction. The protein window provided information about the protein and other links related to the protein.