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      A manually curated network of the PML nuclear body interactome reveals an important role for PML-NBs in SUMOylation dynamics

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          Abstract

          Promyelocytic Leukaemia Protein nuclear bodies (PML-NBs) are dynamic nuclear protein aggregates. To gain insight in PML-NB function, reductionist and high throughput techniques have been employed to identify PML-NB proteins. Here we present a manually curated network of the PML-NB interactome based on extensive literature review including database information. By compiling 'the PML-ome', we highlighted the presence of interactors in the Small Ubiquitin Like Modifier (SUMO) conjugation pathway. Additionally, we show an enrichment of SUMOylatable proteins in the PML-NBs through an in-house prediction algorithm. Therefore, based on the PML network, we hypothesize that PML-NBs may function as a nuclear SUMOylation hotspot.

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          Development of human protein reference database as an initial platform for approaching systems biology in humans.

          Suraj Peri, J Navarro, Ramars Amanchy … (2003)
          Human Protein Reference Database (HPRD) is an object database that integrates a wealth of information relevant to the function of human proteins in health and disease. Data pertaining to thousands of protein-protein interactions, posttranslational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellular localization were extracted from the literature for a nonredundant set of 2750 human proteins. Almost all the information was obtained manually by biologists who read and interpreted >300,000 published articles during the annotation process. This database, which has an intuitive query interface allowing easy access to all the features of proteins, was built by using open source technologies and will be freely available at http://www.hprd.org to the academic community. This unified bioinformatics platform will be useful in cataloging and mining the large number of proteomic interactions and alterations that will be discovered in the postgenomic era.
          Article 0 comments Cited 343 times – based on 0 reviews     Review now
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            Is Open Access

            IntAct—open source resource for molecular interaction data

            S. Kerrien, Y. Alam-Faruque, Gloria Aranda … (2006)
            IntAct is an open source database and software suite for modeling, storing and analyzing molecular interaction data. The data available in the database originates entirely from published literature and is manually annotated by expert biologists to a high level of detail, including experimental methods, conditions and interacting domains. The database features over 126 000 binary interactions extracted from over 2100 scientific publications and makes extensive use of controlled vocabularies. The web site provides tools allowing users to search, visualize and download data from the repository. IntAct supports and encourages local installations as well as direct data submission and curation collaborations. IntAct source code and data are freely available from .
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              PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification.

              P. Thomas (2003)
              The PANTHER database was designed for high-throughput analysis of protein sequences. One of the key features is a simplified ontology of protein function, which allows browsing of the database by biological functions. Biologist curators have associated the ontology terms with groups of protein sequences rather than individual sequences. Statistical models (Hidden Markov Models, or HMMs) are built from each of these groups. The advantage of this approach is that new sequences can be automatically classified as they become available. To ensure accurate functional classification, HMMs are constructed not only for families, but also for functionally distinct subfamilies. Multiple sequence alignments and phylogenetic trees, including curator-assigned information, are available for each family. The current version of the PANTHER database includes training sequences from all organisms in the GenBank non-redundant protein database, and the HMMs have been used to classify gene products across the entire genomes of human, and Drosophila melanogaster. The ontology terms and protein families and subfamilies, as well as Drosophila gene c;assifications, can be browsed and searched for free. Due to outstanding contractual obligations, access to human gene classifications and to protein family trees and multiple sequence alignments will temporarily require a nominal registration fee. PANTHER is publicly available on the web at http://panther.celera.com.
              Article 0 comments Cited 228 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Int J Biol Sci
                Journal ID (publisher-id): ijbs
                Title: International Journal of Biological Sciences
                Publisher: Ivyspring International Publisher (Sydney )
                ISSN (Electronic): 1449-2288
                Publication date Collection: 2010
                Publication date (Electronic): 12 January 2010
                Volume: 6
                Issue: 1
                Pages: 51-67
                Affiliations
                1. Laboratory of Protein Chemistry, Proteomics and Signal Transduction, Department of Biomedical Sciences, University of Antwerp (Campus Drie Eiken), Universiteitsplein 1 - Building T, 2610 Wilrijk, Belgium.
                2. Intelligent Systems Laboratory (ISLab) Department of Mathematics and Computer Science, University of Antwerp (Campus Middelheim), Middelheimlaan 1 - Building G, 2020 Antwerp, Belgium
                Author notes
                ✉ Correspondence to: Prof. Dr. Xaveer Van Ostade, xaveer.vanostade@ 123456ua.ac.be , tel: 0032 (0)3 365 23 19

                Conflict of Interest: The authors have declared that no conflict of interest exists.

                Article
                Publisher ID: ijbsv06p0051
                DOI: 10.7150/ijbs.6.51
                PMC ID: 2808052
                PubMed ID: 20087442
                SO-VID: bfe816a8-b0c8-4907-b8be-3ff3b77cc88e
                Copyright © © Ivyspring International Publisher. This is an open-access article distributed under the terms of the Creative Commons License (http://creativecommons.org/licenses/by-nc-nd/3.0/). Reproduction is permitted for personal, noncommercial use, provided that the article is in whole, unmodified, and properly cited.
                History
                Date received : 20 October 2009
                Date accepted : 9 January 2010
                Categories
                Subject: Review

                ScienceOpen disciplines: Life sciences
                Keywords: network,protein-protein interaction,cytoscape,sumoylation,pml-nb
                Data availability:
                ScienceOpen disciplines: Life sciences
                Keywords: network, protein-protein interaction, cytoscape, sumoylation, pml-nb

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