www.jcvi.org/mpidb johannes goll acknowledgements j. craig venter institute dr. linda hannick shelby...

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