ArticleDatabase : the journal of biological databases and curation2016
UbiNet: an online resource for exploring the functional associations and regulatory networks of protein ubiquitylation.
Article in Database : the journal of biological databases and curation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 34 citations in OpenAlex.
- Ubigo-X: Protein ubiquitination site prediction using ensemble learning with image-based feature representation and weighted voting.Computational and structural biotechnology journal · 2025Article
- The RNF214-TEAD-YAP signaling axis promotes hepatocellular carcinoma progression via TEAD ubiquitylation.Nature communications · 2024Article
- Article
- Integrin-Driven Axon Regeneration in the Spinal Cord Activates a Distinctive CNS Regeneration Program.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2023Article
- Calpain activity is negatively regulated by a KCTD7-Cullin-3 complex via non-degradative ubiquitination.Cell discovery · 2023Article
- CRL4Cancers · 2022Review
- Review
- Prediction and analysis of multiple protein lysine modified sites based on conditional wasserstein generative adversarial networks.BMC bioinformatics · 2021Article
- 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
- Highly Specialized Ubiquitin-Like Modifications: Shedding Light into the UFM1 Enigma.Biomolecules · 2021Review
- Functional Genomics Identify Distinct and Overlapping Genes Mediating Resistance to Different Classes of Heterobifunctional Degraders of Oncoproteins.Cell reports · 2021Article
- Prognostic Role of the Ubiquitin Proteasome System in Clear Cell Renal Cell Carcinoma: A Bioinformatic Perspective.Journal of Cancer · 2021Article
- Emerging Links between Control of Mitochondrial Protein ATAD3A and Cancer.International journal of molecular sciences · 2020Review
- Advances on Plant Ubiquitylome-From Mechanism to Application.International journal of molecular sciences · 2020Review
- Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches.Briefings in bioinformatics · 2019Review
- dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications.Nucleic acids research · 2019Article
- Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions.BMC systems biology · 2017Article
- Protein post-translational modifications:Computational and structural biotechnology journal · 2017Review
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Authors and funding
5 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein ubiquitylation catalyzed by E3 ubiquitin ligases are crucial in the regulation of many cellular processes. Owing to the high throughput of mass spectrometry-based proteomics, a number of methods have been developed for the experimental determination of ubiquitylation sites, leading to a large collection of ubiquitylation data. However, there exist no resources for the exploration of E3-ligase-associated regulatory networks of for ubiquitylated proteins in humans. Therefore, the UbiNet database was developed to provide a full investigation of protein ubiquitylation networks by incorporating experimentally verified E3 ligases, ubiquitylated substrates and protein-protein interactions (PPIs). To date, UbiNet has accumulated 43 948 experimentally verified ubiquitylation sites from 14 692 ubiquitylated proteins of humans. Additionally, we have manually curated 499 E3 ligases as well as two E1 activating and 46 E2 conjugating enzymes. To delineate the regulatory networks among E3 ligases and ubiquitylated proteins, a total of 430 530 PPIs were integrated into UbiNet for the exploration of ubiquitylation networks with an interactive network viewer. A case study demonstrated that UbiNet was able to decipher a scheme for the ubiquitylation of tumor proteins p63 and p73 that is consistent with their functions. Although the essential role of Mdm2 in p53 regulation is well studied, UbiNet revealed that Mdm2 and additional E3 ligases might be implicated in the regulation of other tumor proteins by protein ubiquitylation. Moreover, UbiNet could identify potential substrates for a specific E3 ligase based on PPIs and substrate motifs. With limited knowledge about the mechanisms through which ubiquitylated proteins are regulated by E3 ligases, UbiNet offers users an effective means for conducting preliminary analyses of protein ubiquitylation. The UbiNet database is now freely accessible via http://csb.cse.yzu.edu.tw/UbiNet/ The content is regularly updated with the literature and newly released data.Database URL: http://csb.cse.yzu.edu.tw/UbiNet/.
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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.