www.jcvi.org/mpidb johannes goll acknowledgements j. craig venter institute dr. linda hannick shelby...
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www.jcvi.org/mpidb
Johannes Goll
Acknowledgements
J. Craig Venter InstituteDr. Linda HannickShelby BidwellLis CalerGranger SuttonSeesandra RajagopalaPeter Uetz
European Bioinformatics InstituteBruno Aranda Samuel Kerrien Henning Hermjakob Sandra Orchard
Georgetown UniversityHongfang Liu
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High-throughput Experiments
Complex Purification
Y2H
http://www.ebi.ac.uk/intact
Small Scale Experiments
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Functional Characterization of Proteins
Rajagopala et al. (2006)
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Network Analysis (Modules, Drug Targets, Evolution)
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24,295
26,57868,346
MPIDB Conceptual Overview
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BLASTP
all-against-all
(7,810 proteins)
E-Value<1E-5
62,541Interolog evidences
Matthews et al. (2001)
24,295 MPIDBinteractions
24,295 MPIDBinteractions
Interolog Evidences
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Hakes et al. (2006)
Complex Purification
24,295 MPIDBinteractions
2,497co-purification
evidences
Matrix predictions (c)
Co-Purification Evidences
A Real Complex Topology
B Spoke Model
C Matrix Model
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Domain-Domain Interaction Evidences
Protein B
Protein A
PF00842 - PF01168
<5 Angstroem
iPfam & 3DID database
(predicted domain contacts)
Protein A Protein B
PF01168 PF00842
PF03098 PF01315
PF01168
22,530 MPIDBinteractions
Added 3,082 evidences
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MPIDB – Demo: How to search for a protein
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MPIDB – Demo : Search Results
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http://groel
MPIDB – Demo : Interaction Evidences
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PSICQUIC Web Service Cytoscape 2.7.0 Plugin
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Literature Curation
IMEx - The International Molecular Exchange Consortium http://www.imexconsortium.org/
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Issues 95Articles 1286Positive Articles 171Experiment Entries 291Proteins Entries 600Unique proteins 506Interaction Entries 717Unique interactions 549Feature Entries 67Avg. Time Per Article 36 minAvg. Articles Per Hour 1.9
Literature Curation Statistics
Top Ten Experimental Methods
Top Ten Species
Relevant Articles
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Outlook
SBGN Graphical Format Example Binary Network Data
Textbook Figures
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Questions ?
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Motivation
Collection of all known microbial interactions
data integration: known interactions are spread over several interaction databases users need to query several datasets to gather all interactions
small scale reference interactions: ‘true positive’ reference set of microbial interactions curated from the literature
publication resource: for JCVI’s experimental protein-protein interactions
To answer questions like
Does my protein of interest have known interaction partners?
Is my favourite interaction conserved in another species?
Have my interacting proteins been co-crystalized in a 3D structure?
Can I trust this experimental interaction result? ...
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Outline
Background & Motivation
MPIDB Data – interactions, experiments & additional evidences
MPIDB Web Interface
MPIDB Literature Curation Projects
Outlook
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MPIDB – Protein Interaction Curation Interface | Publication Display