ArticleMolecular & cellular proteomics : MCP2012
E3Net: a system for exploring E3-mediated regulatory networks of cellular functions.
Article in Molecular & cellular proteomics : MCP, 2012. 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, 44 citations in OpenAlex.
- SARS-CoV-2 ORF3a suppresses host antiviral interferon responses by promoting STUB1-mediated PTEN proteasomal degradation.Journal of virology · 2026Article
- Multi-scale classification decodes the complexity of the human E3 ligome.Nature communications · 2025Article
- A structurally informed human protein-protein interactome reveals proteome-wide perturbations caused by disease mutations.Nature biotechnology · 2025Article
- Myofibrillogenesis Regulator-1 Regulates the Ubiquitin Lysosomal Pathway of Notch3 Intracellular Domain Through E3 Ubiquitin-Protein Ligase Itchy Homolog in the Metastasis of Non-Small Cell Lung Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Structurally-informed human interactome reveals proteome-wide perturbations by disease mutations.bioRxiv : the preprint server for biology · 2024Article
- Deep-learning based approach to identify substrates of human E3 ubiquitin ligases and deubiquitinases.Computational and structural biotechnology journal · 2023Article
- Systematic prediction of degrons and E3 ubiquitin ligase binding via deep learning.BMC biology · 2022Article
- UbiNet 2.0: a verified, classified, annotated and updated database of E3 ubiquitin ligase-substrate interactions.Database : the journal of biological databases and curation · 2021Article
- Crosstalk and ultrasensitivity in protein degradation pathways.PLoS computational biology · 2020Article
- Systematic analysis of alterations in the ubiquitin proteolysis system reveals its contribution to driver mutations in cancer.Nature cancer · 2020Article
- dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications.Nucleic acids research · 2019Article
- An integrated bioinformatics platform for investigating the human E3 ubiquitin ligase-substrate interaction network.Nature communications · 2017Article
- A new scheme to discover functional associations and regulatory networks of E3 ubiquitin ligases.BMC systems biology · 2016Article
- dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins.Nucleic acids research · 2016Article
- UbiNet: an online resource for exploring the functional associations and regulatory networks of protein ubiquitylation.Database : the journal of biological databases and curation · 2016Article
- Disease association and inter-connectivity analysis of human brain specific co-expressed functional modules.Biological research · 2015Article
- Detection and analysis of disease-associated single nucleotide polymorphism influencing post-translational modification.BMC medical genomics · 2015Article
- Ubiquitin sets the timer: impacts on aging and longevity.Nature structural & molecular biology · 2014Review
- HMPAS: Human Membrane Protein Analysis System.Proteome science · 2013Article
- UUCD: a family-based database of ubiquitin and ubiquitin-like conjugation.Nucleic acids research · 2013Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ubiquitin-protein ligase (E3) is a key enzyme targeting specific substrates in diverse cellular processes for ubiquitination and degradation. The existing findings of substrate specificity of E3 are, however, scattered over a number of resources, making it difficult to study them together with an integrative view. Here we present E3Net, a web-based system that provides a comprehensive collection of available E3-substrate specificities and a systematic framework for the analysis of E3-mediated regulatory networks of diverse cellular functions. Currently, E3Net contains 2201 E3s and 4896 substrates in 427 organisms and 1671 E3-substrate specific relations between 493 E3s and 1277 substrates in 42 organisms, extracted mainly from MEDLINE abstracts and UniProt comments with an automatic text mining method and additional manual inspection and partly from high throughput experiment data and public ubiquitination databases. The significant functions and pathways of the extracted E3-specific substrate groups were identified from a functional enrichment analysis with 12 functional category resources for molecular functions, protein families, protein complexes, pathways, cellular processes, cellular localization, and diseases. E3Net includes interactive analysis and navigation tools that make it possible to build an integrative view of E3-substrate networks and their correlated functions with graphical illustrations and summarized descriptions. As a result, E3Net provides a comprehensive resource of E3s, substrates, and their functional implications summarized from the regulatory network structures of E3-specific substrate groups and their correlated functions. This resource will facilitate further in-depth investigation of ubiquitination-dependent regulatory mechanisms. E3Net is freely available online at http://pnet.kaist.ac.kr/e3net.
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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.