mentha: a resource for browsing integrated protein-interaction networks
TLDR
Systems-level approaches require access to comprehensive genome-wide and proteome-wide databases and a comprehensive resource that archives all published protein-protein interactions (PPIs) is not available.Abstract:
Systems-level approaches require access to comprehensive
genome-wide and proteome-wide databases. A comprehensive
resource that archives all published protein-protein interactions
(PPIs) is not available. In fact, primary PPI databases capture
only a fraction of published data.read more
Citations
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Journal ArticleDOI
The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.
Sandra Orchard,Mais G. Ammari,Bruno Aranda,Lionel Breuza,Leonardo Briganti,Fiona Broackes-Carter,Nancy H. Campbell,Gayatri Chavali,Carol Chen,Noemi del-Toro,Margaret Duesbury,Marine Dumousseau,Eugenia Galeota,Ursula Hinz,Marta Iannuccelli,Sruthi Jagannathan,Rafael C. Jimenez,Jyoti Khadake,Astrid Lagreid,Luana Licata,Ruth C. Lovering,Birgit H M Meldal,Anna N. Melidoni,Mila Milagros,Daniele Peluso,Livia Perfetto,Pablo Porras,Arathi Raghunath,Sylvie Ricard-Blum,Bernd Roechert,Andre Stutz,Michael Tognolli,Kim Van Roey,Gianni Cesareni,Henning Hermjakob +34 more
TL;DR: All data manually curated by the MINT curators have been moved into the IntAct database at EMBL-EBI and are merged with the existing IntAct dataset.
Journal ArticleDOI
A reference map of the human binary protein interactome
Katja Luck,Dae-Kyum Kim,Luke Lambourne,Kerstin Spirohn,Bridget E. Begg,Wenting Bian,Ruth Brignall,Tiziana M. Cafarelli,Francisco J. Campos-Laborie,Benoit Charloteaux,Dong-Sic Choi,Atina G. Cote,Meaghan Daley,Steven Deimling,Alice Desbuleux,Amélie Dricot,Marinella Gebbia,Madeleine F. Hardy,Nishka Kishore,Jennifer J. Knapp,István Kovács,István Kovács,Irma Lemmens,Irma Lemmens,Miles W. Mee,Joseph C. Mellor,Carl Pollis,Carles Pons,Aaron Richardson,Sadie Schlabach,Bridget Teeking,Anupama Yadav,Mariana Babor,Dawit Balcha,Omer Basha,Christian Bowman-Colin,Suet-Feung Chin,Soon Gang Choi,Claudia Colabella,Georges Coppin,Cassandra D’Amata,David De Ridder,Steffi De Rouck,Steffi De Rouck,Miquel Duran-Frigola,Hanane Ennajdaoui,Florian Goebels,Liana Goehring,Anjali Gopal,Ghazal Haddad,Elodie Hatchi,Mohamed Helmy,Yves Jacob,Yves Jacob,Yoseph Kassa,Serena Landini,Roujia Li,Natascha van Lieshout,Andrew MacWilliams,Dylan Markey,Joseph N. Paulson,Joseph N. Paulson,Sudharshan Rangarajan,John Rasla,Ashyad Rayhan,Thomas Rolland,Adriana San-Miguel,Yun Shen,Dayag Sheykhkarimli,Gloria M. Sheynkman,Eyal Simonovsky,Murat Tasan,Alexander O. Tejeda,Vincent Tropepe,Jean-Claude Twizere,Yang Wang,Robert J. Weatheritt,Jochen Weile,Yu Xia,Yu Xia,Xinping Yang,Esti Yeger-Lotem,Quan Zhong,Patrick Aloy,Gary D. Bader,Javier De Las Rivas,Suzanne Gaudet,Tong Hao,Janusz Rak,Jan Tavernier,Jan Tavernier,David E. Hill,Marc Vidal,Frederick P. Roth,Michael A. Calderwood +94 more
TL;DR: The utility of HuRI is demonstrated in identifying the specific subcellular roles of protein–protein interactions and in identifying potential molecular mechanisms that might underlie tissue-specific phenotypes of Mendelian diseases.
Journal ArticleDOI
A scored human protein–protein interaction network to catalyze genomic interpretation
Taibo Li,Rasmus Wernersson,Rasmus Borup Hansen,Heiko Horn,Heiko Horn,Johnathan Mercer,Johnathan Mercer,Grzegorz Slodkowicz,Christopher T. Workman,Olga Rigina,Kristoffer Rapacki,Hans Henrik Stærfeldt,Søren Brunak,Thomas Skøt Jensen,Kasper Lage +14 more
TL;DR: It is illustrated that InWeb_InBioMap enables functional interpretation of >4,700 cancer genomes and genes involved in autism and better functional biological relevance than comparable resources.
Journal ArticleDOI
OmniPath: guidelines and gateway for literature-curated signaling pathway resources
TL;DR: The results show consistency among literature curated resources, biological properties of the proteins and interactions covered, and the combined network: Omnipath and pypath.
Journal ArticleDOI
SIGNOR: A database of causal relationships between biological entities
Livia Perfetto,Leonardo Briganti,Alberto Calderone,Andrea Cerquone Perpetuini,Marta Iannuccelli,Francesca Langone,Luana Licata,Milica Marinkovic,Anna Mattioni,Theodora Pavlidou,Daniele Peluso,Lucia Lisa Petrilli,Stefano Pirrò,Daniela Posca,Elena Santonico,Alessandra Silvestri,Filomena Spada,Luisa Castagnoli,Gianni Cesareni +18 more
TL;DR: Assembly of large biochemical networks can be achieved by confronting new cell-specific experimental data with an interaction subspace constrained by prior literature evidence by providing a scaffold of prior experimental evidence of causal relationships between biological entities.
References
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Journal ArticleDOI
MINT, the molecular interaction database: 2012 update
Luana Licata,Leonardo Briganti,Daniele Peluso,Livia Perfetto,Marta Iannuccelli,Eugenia Galeota,Francesca Sacco,A. Palma,Aurelio Pio Nardozza,Elena Santonico,Luisa Castagnoli,Gianni Cesareni +11 more
TL;DR: The growth of the database, the major changes in curation policy and a new algorithm to assign a confidence to each interaction are reported here.
Journal ArticleDOI
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.
Henning Hermjakob,Luisa Montecchi-Palazzi,Gary D. Bader,Jérôme Wojcik,Lukasz Salwinski,Arnaud Ceol,Susan Moore,Sandra Orchard,Ugis Sarkans,Christian von Mering,Bernd Roechert,Sylvain Poux,Eva Jung,Henning Mersch,Paul J. Kersey,Michael Lappe,Yixue Li,Rong Zeng,Debashis Rana,Macha Nikolski,Holger Husi,Christine Brun,K. Shanker,Seth G. N. Grant,Chris Sander,Peer Bork,Weimin Zhu,Akhilesh Pandey,Alvis Brazma,Bernard Jacq,Marc Vidal,David James Sherman,Pierre Legrain,Gianni Cesareni,Ioannis Xenarios,David Eisenberg,Boris Steipe,Christopher W. V. Hogue,Rolf Apweiler +38 more
TL;DR: This work proposes a community standard data model for the representation and exchange of protein interaction data, jointly developed by members of the Proteomics Standards Initiative (PSI) and the Human Proteome Organization (HUPO).
Journal ArticleDOI
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium
Sandra Orchard,Samuel Kerrien,Sara Abbani,Bruno Aranda,Jignesh Bhate,Shelby L. Bidwell,Alan Bridge,Leonardo Briganti,Fiona S. L. Brinkman,Gianni Cesareni,Andrew Chatr-aryamontri,Andrew Chatr-aryamontri,Emilie Chautard,Emilie Chautard,Carol Chen,Marine Dumousseau,Johannes B. Goll,Robert E. W. Hancock,Linda Hannick,Igor Jurisica,Jyoti Khadake,David J. Lynn,Usha Mahadevan,Livia Perfetto,Arathi Raghunath,Sylvie Ricard-Blum,Bernd Roechert,Lukasz Salwinski,Volker Stümpflen,Mike Tyers,Mike Tyers,Peter Uetz,Ioannis Xenarios,Ioannis Xenarios,Henning Hermjakob +34 more
TL;DR: The International Molecular Exchange consortium is an international collaboration between major public interaction data providers to share literature-curation efforts and make a nonredundant set of protein interactions available in a single search interface on a common website.
Journal ArticleDOI
PSICQUIC and PSISCORE: accessing and scoring molecular interactions
Bruno Aranda,Hagen Blankenburg,Samuel Kerrien,Fiona S. L. Brinkman,Arnaud Ceol,Emilie Chautard,Jose M. Dana,Javier De Las Rivas,Marine Dumousseau,Eugenia Galeota,Anna Gaulton,Johannes B. Goll,Robert E. W. Hancock,Ruth Isserlin,Rafael C. Jimenez,Jules Kerssemakers,Jyoti Khadake,David J. Lynn,Magali Michaut,Gavin O'Kelly,Keiichiro Ono,Sandra Orchard,Carlos Prieto,Sabry Razick,Olga Rigina,Lukasz Salwinski,Milan Simonovic,Sameer Velankar,Andrew G. Winter,Guanming Wu,Gary D. Bader,Gianni Cesareni,Ian Donaldson,David Eisenberg,Gerard J. Kleywegt,John P. Overington,Sylvie Ricard-Blum,Mike Tyers,Mario Albrecht,Henning Hermjakob +39 more
TL;DR: To study proteins in the context of a cellular system, it is essential that the molecules with which a protein interacts are identified and the functional consequence of each interaction is understood.
Journal ArticleDOI
Recurated protein interaction datasets.
Lukasz Salwinski,Luana Licata,Andrew G. Winter,David Thorneycroft,Jyoti Khadake,Arnaud Ceol,Andrew Chatr Aryamontri,Rose Oughtred,Michael S. Livstone,Lorrie Boucher,David Botstein,Kara Dolinski,Tanya Z. Berardini,Eva Huala,Mike Tyers,Mike Tyers,David Eisenberg,Gianni Cesareni,Henning Hermjakob +18 more
TL;DR: In response to the claims of Cusick et al.1, reanalyzed interactions presented in their paper to identify actual curation errors, defined as inconsistencies between the original published data and their representation in the authors' databases.
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The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.
Sandra Orchard,Mais G. Ammari,Bruno Aranda,Lionel Breuza,Leonardo Briganti,Fiona Broackes-Carter,Nancy H. Campbell,Gayatri Chavali,Carol Chen,Noemi del-Toro,Margaret Duesbury,Marine Dumousseau,Eugenia Galeota,Ursula Hinz,Marta Iannuccelli,Sruthi Jagannathan,Rafael C. Jimenez,Jyoti Khadake,Astrid Lagreid,Luana Licata,Ruth C. Lovering,Birgit H M Meldal,Anna N. Melidoni,Mila Milagros,Daniele Peluso,Livia Perfetto,Pablo Porras,Arathi Raghunath,Sylvie Ricard-Blum,Bernd Roechert,Andre Stutz,Michael Tognolli,Kim Van Roey,Gianni Cesareni,Henning Hermjakob +34 more
Human Protein Reference Database—2009 update
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Gene Ontology: tool for the unification of biology
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