ArticleScientific reports2015
Genome-wide protein-protein interactions and protein function exploration in cyanobacteria.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 29 citations in OpenAlex.
- The genome of Symbiodiniaceae-associated Stutzerimonas frequens CAM01 reveals a broad spectrum of antibiotic resistance genes indicating anthropogenic drift in the Palk Bay coral reef of south-eastern India.Archives of microbiology · 2023Article
- Deep Proteogenomics of a Photosynthetic Cyanobacterium.Journal of proteome research · 2023Article
- Global Landscape of Native Protein Complexes in Synechocystis sp. PCC 6803.Genomics, proteomics & bioinformatics · 2022Article
- Computational Network Inference for Bacterial Interactomics.mSystems · 2022Review
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- Network analyses in microbiome based on high-throughput multi-omics data.Briefings in bioinformatics · 2021Review
- Protein functional annotation of simultaneously improved stability, accuracy and false discovery rate achieved by a sequence-based deep learning.Briefings in bioinformatics · 2020Article
- Emerging Species and Genome Editing Tools: Future Prospects in Cyanobacterial Synthetic Biology.Microorganisms · 2019Review
- New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering.Frontiers in bioengineering and biotechnology · 2019Review
- Article
- Phylo_dCor: distance correlation as a novel metric for phylogenetic profiling.BMC bioinformatics · 2017Article
- Large-scale identification of human protein function using topological features of interaction network.Scientific reports · 2016Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome-wide network analysis is well implemented to study proteins of unknown function. Here, we effectively explored protein functions and the biological mechanism based on inferred high confident protein-protein interaction (PPI) network in cyanobacteria. We integrated data from seven different sources and predicted 1,997 PPIs, which were evaluated by experiments in molecular mechanism, text mining of literatures in proved direct/indirect evidences, and "interologs" in conservation. Combined the predicted PPIs with known PPIs, we obtained 4,715 no-redundant PPIs (involving 3,231 proteins covering over 90% of genome) to generate the PPI network. Based on the PPI network, terms in Gene ontology (GO) were assigned to function-unknown proteins. Functional modules were identified by dissecting the PPI network into sub-networks and analyzing pathway enrichment, with which we investigated novel function of underlying proteins in protein complexes and pathways. Examples of photosynthesis and DNA repair indicate that the network approach is a powerful tool in protein function analysis. Overall, this systems biology approach provides a new insight into posterior functional analysis of PPIs in cyanobacteria.
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