Function Annotation of Proteins in Eriocheir sinensis Based on the Protein-Protein Interaction Network

Abstract

Eriocheir sinensis is a highly-commercial aquaculture species as an important aquatic product source. The protein-protein interaction network (PIN) of E. sinensis has been constructed based on the RNA transcriptional sequencing. Many unknown proteins exist in the PIN, which seriously restricts the further mechanism researches on regulation, immunity and development of E. sinensis. In this work, we predicted the functions of the unknown proteins in E. sinensis based on the modularity feature of the PIN. The functions of 677 (93 %) proteins were annotated. The analysis of ribosome module indicates that the annotation of proteins and modules provides important references to be studied in the further in vivo experiment as well as the biological capability of the E. sinensis PIN.

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

“…Similar efforts can be performed in aquaculture research as the PPI network can contribute knowledge related to molecular aspects to this field. For instance, the PPI network adopted in human diseases can also be used to understand the diseases that plague the aquaculture industry by identifying the proteins responsible for aquatic diseases (i.e., white spot disease in the penaeid shrimps that cause by a white spot syndrome virus (WSSV)) [ 25 , 26 ]. It can also be used to predict the pathogenesis of the diseases, which is essential to improve disease prognosis and diagnosis and design targeted antibacterial drugs in Nile tilapia, Oreochromis niloticus [ 27 ].…”

“…It can also be used to predict the pathogenesis of the diseases, which is essential to improve disease prognosis and diagnosis and design targeted antibacterial drugs in Nile tilapia, Oreochromis niloticus [ 27 ]. In addition, the functional annotation of unknown proteins in aquaculture species can also be predicted using the PPI network [ 25 ]. However, PPI information on aquaculture species remains limited except for a model organism of zebrafish, Danio rerio.…”