The microbial protein interaction database (MPIDB) aims
to collect and provide all known physical microbial interactions.
Currently, 24,295 experimentally determined interactions among
proteins of 250 bacterial species/strains can be browsed and
downloaded. These microbial interactions have been manually
curated from the literature or imported from other databases (IntAct,
DIP, BIND, MINT) and are linked to 26,578 experimental evidences
(PubMed ID, PSI-MI methods). In contrast to these databases,
interactions in MPIDB are further supported by 68,346 additional
evidences based on interaction conservation, protein complex membership, and 3D
domain contacts (iPfam, 3did). We do not include (spoke/matrix) binary interactions
infered from pull-down experiments. MPIDB is a topical member of the IMEx consortium.
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Experimental Evidences
Experimental evidences are based on interaction experiments that identified two proteins.
An experimental evidence is defined by its experimental interaction detection method (PSI-MI controlled vocabulary)
in combination with its publication (PubMed ID). Experiments from pull-down studies were only included if a
bait protein identified only one prey protein. Overall, we collected 26,578 experimental evidences that describe
a unique set of 24,295 protein-protein interactions. The number of non-redundand interactions per database/dataset
is given below:
Version/Date |
Interactions |
Source Database |
Description |
2007-04-06 |
1,563 |
BIND |
The Biomolecular Interaction Network Database |
2008-10-14 |
2,109 |
DIP |
Database of Interacting Proteins |
2009-10-09 |
20,419 |
IntAct |
Open Source Resource for Molecular Interaction Data |
2009-07-28 |
2,070 |
MINT |
Molecular Interactions Database |
2008-04-06 |
745 |
MPI-LIT |
MPIDB's MPI-LIT literature curated dataset. Read more |
2009-11-18 |
3,814 |
MPI-EXP |
MPIDB's Y2H experimental microbial dataset. |
2009-11-18 |
473 |
MPI-IMEX |
MPIDB's IMEx literature curated dataset. As a topical member of IMEx, MPIDB curates interactions from two journals: Journal of Bacterology and Molecular Microbiology. |
2009-11-18 |
5,032 |
MPIDB Total |
MPI-LIT & MPI-EXP & MPI-IMEX |
Additional Evidences
The set of 24,295 protein-protein interactions was screened for conservation in the same or another species (Interologs),
for potential interacting domain pairs (Structural Domain Contacts), for protein complex membership,
and for secondary citations. Overall we added 68,346 additional evidences. The number of evidences per method is given below:
Number of Additional Evidences |
Evidence Type |
Description |
62,541 |
Interologs |
Interactions were used to identify homologous interactions (interologs) in the same or another species.
A protein sequence comparison of interacting proteins revealed 62,541 pairwise homologous relationships among interactions
(BLAST E-Value cut off E=< 1x10-5). |
2,497 |
Protein Complex Memberships |
Binary interactions from protein complexes were predicted based on the matrix model, i.e. all complex proteins are assumed to interact with one another. Protein complex memberships are added to interactions that have at least one direct experimental evidence. The type field indicates the size of the complex. Note: co-purification experiments in which a bait purified only one prey protein are treated as experimental evidence not a protein complex membership evidence. |
3,082 |
Structural Domain Contacts |
Pfam domain combinations that have been found to form close contacts in three-dimensional structures (iPfam, 3DID) |
226 |
Secondary References |
References that have been cited for a certain interaction (without experimental evidence). |
MPIDB's experimental and literature curated datasets
MPI-LIT contains interactions that we have manually curated from over 800 scientific articles. Read more
MPI-EXP contains Y2H interactions identified by JCVI's Uetz Lab. This set currently comprises 3, 640 interactions for Treponema pallidum. Read more.
MPI-IMEX contains interactions that we have curated from 1,284 articles of the latest 98 issues of two journals: Journal of Bacteriology and Molecular Microbiology.
Data Import & Web Site Implementation
MPIDB utilizes the three-tier software engineering architecture, which decouples data, logic, and presentation to allow independent and efficient development and deployment. The data tier resides on a highly available MySQL5 database server cluster. The logic tier is handled by PHP5, the presentation tier by Cascading Style Sheets (CSS), while both are served by a robust Apache HTTP Server running the latest stable version of all software.
Foreign interactions where imported by parsing IntAct, Mint, Dip PSI MI 2.5 files. For BIND, we mapped GI IDs to UniProt accessions and BIND methods to PSI MI controlled vocabulary. The BIND dataset remains stable and is not updated as BIND is discontinued.
We use the latest stable primary UniProt accessions to uniquely identify proteins and their protein sequences. All imported accessions are checked if an update has to be performed. In case there is a one to one mapping for the new accession, we update the old one. Otherwise, we skip the entry and also the interaction.
How to link to MPIDB
(1) display interactions by species, e.g. Escherichia coli
www.jcvi.org/mpidb/interaction.php?species_txtbox=Escherichia+coli
(2) display interactions by protein (common name, locus, UniProt accession)
www.jcvi.org/mpidb/interaction.php?pname=chey
www.jcvi.org/mpidb/interaction.php?pname=TM_0700
www.jcvi.org/mpidb/interaction.php?pname=Q56312
(3) display interaction evidences by interaction
www.jcvi.org/mpidb/experiment.php?interaction_id=MPI-00006B
Acknowledgements
The Microbial Protein Interaction Database relies on many fine resources maintained elsewhere:
UniProt,Gene Ontology,
PDBsum,3DID,
iPfam,
IntAct,BIND,
DIP, MINT,
Pfam
How to cite MPIDB
Please cite the first article if you would like to reference/acknowlege the MPIDB database. Please cite the second article if you would like to reference/acknowlege MPIDB's MPI-LIT dataset.
Goll, J., Rajagopala, S. V., et al.
MPIDB: The microbial protein interaction database
Bioinformatics. 2008 June 13
Rajagopala, S. V., Goll, J. et al.
MPI-LIT: a literature-curated dataset of microbial binary protein-protein interactions.
Bioinformatics. 2008 September 11