Download The Microbial Protein Interaction Database

www.jcvi.org/mpidb
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
Johannes Goll
High-throughput Experiments
Complex Purification
http://www.ebi.ac.uk/intact
Y2H
Small Scale Experiments
Functional Characterization of Proteins
Rajagopala et al. (2006)
Network Analysis (Modules, Drug Targets, Evolution)
MPIDB Conceptual Overview
24,295
26,578
68,346
Interolog Evidences
24,295 MPIDB
interactions
BLASTP
all-against-all
(7,810 proteins)
E-Value<1E-5
24,295 MPIDB
interactions
Matthews et al. (2001)
62,541Interolog
evidences
Co-Purification Evidences
Complex Purification
A Real Complex Topology
B Spoke Model
C Matrix Model
Matrix predictions (c)
24,295 MPIDB
interactions
Hakes et al. (2006)
2,497
co-purification
evidences
Domain-Domain Interaction Evidences
22,530 MPIDB
interactions
Protein A Protein B
PF01168 PF00842
PF03098 PF01315
PF01168
Protein A
Protein B
PF00842 - PF01168
Added 3,082 evidences
<5 Angstroem
iPfam & 3DID database
(predicted domain contacts)
MPIDB – Demo: How to search for a protein
MPIDB – Demo : Search Results
MPIDB – Demo : Interaction Evidences
http://groel
PSICQUIC Web Service Cytoscape 2.7.0 Plugin
Literature Curation
IMEx - The International Molecular Exchange Consortium
http://www.imexconsortium.org/
Literature Curation Statistics
Issues
Articles
Positive Articles
Experiment Entries
Proteins Entries
Unique proteins
Interaction Entries
Unique interactions
Feature Entries
Avg. Time Per Article
Avg. Articles Per Hour
95
1286
171
291
600
506
717
549
67
36 min
1.9
Top Ten Experimental Methods
adenylate cyclase complementation
coimmunoprecipitation
two hybrid
pull down
genetic interference
cross-linking study
affinity chromatography technology
far western blotting
experimental interaction detection
molecular sieving
0
5
10
15
20
25
30
35
40
Top Ten Species
Escherichia coli (strain K12)
Relevant Articles
Bacillus subtilis
Pseudomonas aeruginosa
13%
Helicobacter pylori
Synechocystis sp. (strain PCC 6803)
no interactions
interactions
87%
Homo sapiens
Streptomyces coelicolor
Streptococcus pneumoniae
Escherichia coli
Mycobacterium avium (strain 104)
0
20
40
60
80 100 120 140 160 180
Outlook
Binary Network Data
Textbook Figures
SBGN Graphical Format Example
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