ArticleBMC bioinformatics2017
Prediction of GCRV virus-host protein interactome based on structural motif-domain interactions.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 50 citations in OpenAlex.
- Exogenous interactome analysis of bovine viral diarrhea virus-host using network based-approach and identification of hub genes and important pathways involved in virus pathogenesis.Biochemistry and biophysics reports · 2024Article
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- Emvirus: An embedding-based neural framework for human-virus protein-protein interactions prediction.Biosafety and health · 2023Article
- Determining human-coronavirus protein-protein interaction using machine intelligence.Medicine in novel technology and devices · 2023Article
- A correlation coefficient-based feature selection approach for virus-host protein-protein interaction prediction.PloS one · 2023Article
- How different viruses perturb host cellular machinery via short linear motifs.EXCLI journal · 2023Review
- Deep Learning-Powered Prediction of Human-Virus Protein-Protein Interactions.Frontiers in microbiology · 2022Article
- LGCA-VHPPI: A local-global residue context aware viral-host protein-protein interaction predictor.PloS one · 2022Article
- Grass Carp Reovirus VP56 Allies VP4, Recruits, Blocks, and Degrades RIG-I to More Effectively Attenuate IFN Responses and Facilitate Viral Evasion.Microbiology spectrum · 2021Article
- Computational Biology and Machine Learning Approaches to Understand Mechanistic Microbiome-Host Interactions.Frontiers in microbiology · 2021Review
- Article
- Study of combining virtual screening and antiviral treatments of the Sars-CoV-2 (Covid-19).Microbial pathogenesis · 2020Review
- HMI-PRED: A Web Server for Structural Prediction of Host-Microbe Interactions Based on Interface Mimicry.Journal of molecular biology · 2020Article
- Grass Carp Reovirus Major Outer Capsid Protein VP4 Interacts with RNA Sensor RIG-I to Suppress Interferon Response.Biomolecules · 2020Article
- Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved Functional Regions of Viral Proteins.Viruses · 2020Article
- Prediction of human-virus protein-protein interactions through a sequence embedding-based machine learning method.Computational and structural biotechnology journal · 2020Article
- Interface-Based Structural Prediction of Novel Host-Pathogen Interactions.Methods in molecular biology (Clifton, N.J.) · 2019Article
- Inter-Species/Host-Parasite Protein Interaction Predictions Reviewed.Current bioinformatics · 2018Review
- Proteome-wide analysis of human motif-domain interactions mapped on influenza a virus.BMC bioinformatics · 2018Article
- Circular RNAs: A novel type of non-coding RNA and their potential implications in antiviral immunity.International journal of biological sciences · 2017Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGrass carp hemorrhagic disease, caused by grass carp reovirus (GCRV), is the most fatal causative agent in grass carp aquaculture. Protein-protein interactions between virus and host are one avenue through which GCRV can trigger infection and induce disease. Experimental approaches for the detection of host-virus interactome have many inherent limitations, and studies on protein-protein interactions between GCRV and its host remain rare.
resultsIn this study, based on known motif-domain interaction information, we systematically predicted the GCRV virus-host protein interactome by using motif-domain interaction pair searching strategy. These proteins derived from different domain families and were predicted to interact with different motif patterns in GCRV. JAM-A protein was successfully predicted to interact with motifs of GCRV Sigma1-like protein, and shared the similar binding mode compared with orthoreovirus. Differentially expressed genes during GCRV infection process were extracted and mapped to our predicted interactome, the overlapped genes displayed different tissue expression distributions on the whole, the overall expression level in intestinal is higher than that of other three tissues, which may suggest that the functions of these genes are more active in intestinal. Function annotation and pathway enrichment analysis revealed that the host targets were largely involved in signaling pathway and immune pathway, such as interferon-gamma signaling pathway, VEGF signaling pathway, EGF receptor signaling pathway, B cell activation, and T cell activation.
conclusionsAlthough the predicted PPIs may contain some false positives due to limited data resource and poor research background in non-model species, the computational method still provide reasonable amount of interactions, which can be further validated by high throughput experiments. The findings of this work will contribute to the development of system biology for GCRV infectious diseases, and help guide the identification of novel receptors of GCRV in its host.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.