www.jcvi.org/mpidb Johannes Goll Acknowledgements J. Craig Venter Institute Dr. Linda Hannick Shelby Bidwell Lis Caler Granger Sutton Seesandra Rajagopala Peter Uetz European Bioinformatics Institute Bruno Aranda Samuel Kerrien Henning Hermjakob Sandra Orchard Georgetown University Hongfang Liu
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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
High-throughput Experiments
Complex Purification
Y2H
http://www.ebi.ac.uk/intact
Small Scale Experiments
Functional Characterization of Proteins
Rajagopala et al. (2006)
Network Analysis (Modules, Drug Targets, Evolution)
24,295
26,57868,346
MPIDB Conceptual Overview
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
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
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
MPIDB – Demo: How to search for a protein
MPIDB – Demo : Search Results
http://groel
MPIDB – Demo : Interaction Evidences
PSICQUIC Web Service Cytoscape 2.7.0 Plugin
Literature Curation
IMEx - The International Molecular Exchange Consortium http://www.imexconsortium.org/
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
Outlook
SBGN Graphical Format Example Binary Network Data
Textbook Figures
Questions ?
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? ...
Outline
Background & Motivation
MPIDB Data – interactions, experiments & additional evidences
MPIDB Web Interface
MPIDB Literature Curation Projects
Outlook
MPIDB – Protein Interaction Curation Interface | Publication Display