An evaluation of human protein-protein interaction data in the public domain
Suresh Mathivanan,Suresh Mathivanan,Balamurugan Periaswamy,Balamurugan Periaswamy,T. K. B. Gandhi,Kumaran Kandasamy,Shubha Suresh,Riaz Mohmood,Y. L. Ramachandra,Akhilesh Pandey +9 more
TLDR
It is suggested that submission of PPIs to repositories be made mandatory by scientific journals at the time of manuscript submission as this will minimize annotation errors, promote standardization and help keep the information up to date.Abstract:
Protein-protein interaction (PPI) databases have become a major resource for investigating biological networks and pathways in cells. A number of publicly available repositories for human PPIs are currently available. Each of these databases has their own unique features with a large variation in the type and depth of their annotations. We analyzed the major publicly available primary databases that contain literature curated PPI information for human proteins. This included BIND, DIP, HPRD, IntAct, MINT, MIPS, PDZBase and Reactome databases. The number of binary non-redundant human PPIs ranged from 101 in PDZBase and 346 in MIPS to 11,367 in MINT and 36,617 in HPRD. The number of genes annotated with at least one interactor was 9,427 in HPRD, 4,975 in MINT, 4,614 in IntAct, 3,887 in BIND and <1,000 in the remaining databases. The number of literature citations for the PPIs included in the databases was 43,634 in HPRD, 11,480 in MINT, 10,331 in IntAct, 8,020 in BIND and <2,100 in the remaining databases. Given the importance of PPIs, we suggest that submission of PPIs to repositories be made mandatory by scientific journals at the time of manuscript submission as this will minimize annotation errors, promote standardization and help keep the information up to date. We hope that our analysis will help guide biomedical scientists in selecting the most appropriate database for their needs especially in light of the dramatic differences in their content.read more
Citations
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Human Protein Reference Database—2009 update
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TL;DR: A number of new features in HPRD are added, including PhosphoMotif Finder, which allows users to find the presence of over 320 experimentally verified phosphorylation motifs in proteins of interest, and a protein distributed annotation system—Human Proteinpedia.
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References
More filters
Journal ArticleDOI
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Paul Shannon,Andrew Markiel,Owen Ozier,Nitin S. Baliga,Jonathan T. Wang,Daniel Ramage,Nada Amin,Benno Schwikowski,Trey Ideker +8 more
TL;DR: Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
Journal ArticleDOI
Towards a proteome-scale map of the human protein–protein interaction network
Jean François Rual,Kavitha Venkatesan,Tong Hao,Tomoko Hirozane-Kishikawa,Amélie Dricot,Ning Li,Gabriel F. Berriz,Francis D. Gibbons,Matija Dreze,Nono Ayivi-Guedehoussou,Niels Klitgord,Christophe Simon,Mike Boxem,Stuart Milstein,Jennifer Rosenberg,Debra S. Goldberg,Lan V. Zhang,Sharyl L. Wong,Giovanni Franklin,Siming Li,Joanna S. Albala,Joanna S. Albala,Janghoo Lim,Carlene Fraughton,Estelle Llamosas,Sebiha Cevik,Camille Bex,Philippe Lamesch,Robert S. Sikorski,Jean Vandenhaute,Huda Y. Zoghbi,Alex Smolyar,Stephanie Bosak,Reynaldo Sequerra,Lynn Doucette-Stamm,Michael E. Cusick,David E. Hill,Frederick P. Roth,Marc Vidal +38 more
TL;DR: An initial version of a proteome-scale map of human binary protein–protein interactions is described, which increases by ∼70% the set of available binary interactions within the tested space and reveals more than 300 new connections to over 100 disease-associated proteins.
Journal ArticleDOI
A human protein-protein interaction network : a resource for annotating the proteome
Ulrich Stelzl,Uwe Worm,Maciej Lalowski,Christian Haenig,Felix H. Brembeck,Heike Goehler,Martin Stroedicke,Martina Zenkner,Anke Schoenherr,Susanne Koeppen,Jan Timm,Sascha Mintzlaff,Claudia Abraham,Nicole Bock,Silvia Kietzmann,Astrid Goedde,Engin Toksöz,Anja Droege,Sylvia Krobitsch,Bernhard Korn,Walter Birchmeier,Hans Lehrach,Erich E. Wanker +22 more
TL;DR: A large, highly connected network of interacting pairs of human proteins was identified, characterizing ANP32A and CRMP1 as modulators of Wnt signaling and two novel Axin-1 interactions were validated experimentally.
Journal ArticleDOI
The Database of Interacting Proteins: 2004 update
Lukasz Salwinski,Christopher S. Miller,Adam J. Smith,Frank K. Pettit,James U. Bowie,David Eisenberg +5 more
TL;DR: The Database of Interacting Proteins (DIP; http://dip.doe-mbi.ucla. edu) is a database that documents experimentally determined protein-protein interactions.
Journal ArticleDOI
Reactome: a knowledgebase of biological pathways.
Geeta Joshi-Tope,Marc Gillespie,Marc Gillespie,Imre Vastrik,Peter D'Eustachio,Peter D'Eustachio,Esther Schmidt,B. de Bono,Bijay Jassal,Gopal R. Gopinath,Guanming Wu,Lisa Matthews,Suzanna E. Lewis,Ewan Birney,Lincoln Stein +14 more
TL;DR: The Reactome data model allows us to represent many diverse processes in the human system, including the pathways of intermediary metabolism, regulatory pathways, and signal transduction, and high-level processes, such as the cell cycle.
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