Protein–Protein Interaction (PPI) Network of Zebrafish Oestrogen Receptors: A Bioinformatics Workflow

Abstract

Protein–protein interaction (PPI) is involved in every biological process that occurs within an organism. The understanding of PPI is essential for deciphering the cellular behaviours in a particular organism. The experimental data from PPI methods have been used in constructing the PPI network. PPI network has been widely applied in biomedical research to understand the pathobiology of human diseases. It has also been used to understand the plant physiology that relates to crop improvement. However, the application of the PPI network in aquaculture is limited as compared to humans and plants. This review aims to demonstrate the workflow and step-by-step instructions for constructing a PPI network using bioinformatics tools and PPI databases that can help to predict potential interaction between proteins. We used zebrafish proteins, the oestrogen receptors (ERs) to build and analyse the PPI network. Thus, serving as a guide for future steps in exploring potential mechanisms on the organismal physiology of interest that ultimately benefit aquaculture research.

Integrated analysis reveals the regulatory mechanism of the neddylation inhibitor MLN4924 on the metabolic dysregulation in rabbit granulosa cells

“…MLN4924 has been demonstrated to inhibit the expression of ER-α, a steroid hormone receptor, through SGK1-dependent cytoplasmic localization of FOXO3a [ 49 ]. PPI is composed of proteins that interact with each other, involved in every biological process that occurs within an organism [ 50 ]. Among the top ten key genes in the PPI network, six were involved in regulating cell proliferation and apoptosis, including FGF16, CSF3, GLI1, EDNRB, AVPR2, and FOXM1.…”

In Silico Analysis of Protein–Protein Interactions of Putative Endoplasmic Reticulum Metallopeptidase 1 in Schizosaccharomyces pombe

“…The use of Protein-Protein Interaction (PPI) networks has been instrumental in analyzing the molecular machinery of cells [8,9]. This approach is primarily employed to assign functional roles to potential proteins and to characterize multi-protein complexes and signaling pathways [10].…”

“…In addition to the empirical discovery of PPIs, the comparative strategy of protein interactions conserved across species (interologues) has contributed to the functional annotation of uncharacterized proteins [21]. Although the prediction of human interologues inferred from model organisms is less frequent than expected, the high conservation of small groups of orthologues could be related to highly evolutionarily conserved cellular processes [9,[21][22][23].…”