Identifying protein complexes from protein-protein interaction networks based on the gene expression profile and core-attachment approach.
Published on Apr 28, 2021in Journal of Bioinformatics and Computational Biology1.055
· DOI :10.1142/S0219720021500098
Defining protein complexes in the cell is important for learning about cellular processes mechanisms as they perform many of the molecular functions in these processes. Most of the proposed algorithms predict a complex as a dense area in a Protein-Protein Interaction (PPI) network. Others, on the other hand, weight the network using gene expression or geneontology (GO). These approaches, however, eliminate the proteins and their edges that offer no gene expression data. This can lead to the loss of important topological relations. Therefore, in this study, a method based on the Gene Expression and Core-Attachment (GECA) approach was proposed for addressing these limitations. GECA is a new technique to identify core proteins using common neighbor techniques and biological information. Moreover, GECA improves the attachment technique by adding the proteins that have low closeness but high similarity to the gene expression of the core proteins. GECA has been compared with several existing methods and proved in most datasets to be able to achieve the highest F-measure. The evaluation of complexes predicted by GECA shows high biological significance.