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Database (Oxford). 2011; 2011: bar055.
Published online Nov 30, 2011. doi:  10.1093/database/bar055
PMCID: PMC3228279
hUbiquitome: a database of experimentally verified ubiquitination cascades in humans
Yipeng Du,1,2 Nanfang Xu,1,3 Ming Lu,1 and Tingting Li1,4*
1Department of Medical Informatics, 2Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, 3Peking University First Hospital, Beijing 100034 and 4Institute of Systems Biomedicine, Peking University Health Science Center, Beijing 100191, China
*Corresponding author: Tel: Phone: +86 10 8280 1585; Fax: +86 10 8280 1001; Email: litt/at/hsc.pku.edu.cn
These authors contributed equally to this work.
Received August 25, 2011; Revised October 27, 2011; Accepted November 8, 2011.
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.
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