ArticleDatabase : the journal of biological databases and curation2011
hUbiquitome: a database of experimentally verified ubiquitination cascades in humans.
Article in Database : the journal of biological databases and curation, 2011. 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, 36 citations in OpenAlex.
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- qPTM: an updated database for PTM dynamics in human, mouse, rat and yeast.Nucleic acids research · 2023Article
- Systematic prediction of degrons and E3 ubiquitin ligase binding via deep learning.BMC biology · 2022Article
- UbiBrowser 2.0: a comprehensive resource for proteome-wide known and predicted ubiquitin ligase/deubiquitinase-substrate interactions in eukaryotic species.Nucleic acids research · 2022Article
- Mini-review: Recent advances in post-translational modification site prediction based on deep learning.Computational and structural biotechnology journal · 2022Review
- Cold atmospheric plasmas target breast cancer stemness via modulating AQP3-19Y mediated AQP3-5K and FOXO1 K48-ubiquitination.International journal of biological sciences · 2022Article
- Crosstalk and ultrasensitivity in protein degradation pathways.PLoS computational biology · 2020Article
- A systematic approach to orient the human protein-protein interaction network.Nature communications · 2019Article
- Identification of protein features encoded by alternative exons using Exon Ontology.Genome research · 2017Article
- A bacterial genetic selection system for ubiquitylation cascade discovery.Nature methods · 2016Article
- Comprehensive database of human E3 ubiquitin ligases: application to aquaporin-2 regulation.Physiological genomics · 2016Article
- Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer.Genome medicine · 2016Article
- A new scheme to discover functional associations and regulatory networks of E3 ubiquitin ligases.BMC systems biology · 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
- Biological databases for human research.Genomics, proteomics & bioinformatics · 2015Review
- A method for predicting protein-protein interaction types.PloS one · 2014Article
- Article
- Reconstruction of the experimentally supported human protein interactome: what can we learn?BMC systems biology · 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 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein ubiquitination is an evolutionarily conserved and functionally diverse post-translational modification achieved through the sequential action of E1-activating enzymes, E2-conjugating enzymes and E3 ligases. A summary of validated ubiquitination substrates have been presented and a prediction of new substrates have been conducted in yeast. However, a systematic summary of human ubiquitination substrates containing experimental evidence and the enzymatic cascade of each substrate is not available. In the present study, hUbiquitome web resource is introduced, a public resource for the retrieval of experimentally verified human ubiquitination enzymes and substrates. hUbiquitome is the first comprehensive database of human ubiquitination cascades. Currently, hUbiquitome has in its repertoire curated data comprising 1 E1 enzyme, 12 E2 enzymes, 138 E3 ligases or complexes, 279 different substrate proteins and 17 deubiquitination enzyme terms. The biological functions of substrates from different kinds of E3s were analyzed using the collected data. The findings show that substrates ubiquitinated by RING (Really Interesting New Gene) E3s are enriched most in apoptosis-related processes, whereas substrates ubiquitinated by other E3s are enriched in gene expression-associated processes. An analysis of the data demonstrates the biological process preferences of the different kinds of E3s. hUbiquitome is the first database to systematically collect experimentally validated ubiquitinated proteins and related ubiquitination cascade enzymes which might be helpful in the field of ubiquitination-modification research. Database URL: http://202.38.126.151/hmdd/hubi/
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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.