MPI-LIT: a literature-curated dataset of microbial binary protein--protein interactions.
Prokaryotic protein-protein interactions are underrepresented in currently available databases. Here, we describe a 'gold standard' dataset (MPI-LIT) focusing on microbial binary protein-protein interactions and associated experimental evidence that we have manually curated from 813 abstracts and full texts that were selected from an initial set of 36 852 abstracts. The MPI-LIT dataset comprises 1237 experimental descriptions that describe a non-redundant set of 746 interactions of which 659 (88%) are not reported in public databases. To estimate the curation quality, we compared our dataset with a union of microbial interaction data from IntAct, DIP, BIND and MINT. Among common abstracts, we achieve a sensitivity of up to 66% for interactions and 75% for experimental methods. Compared with these other datasets, MPI-LIT has the lowest fraction of interaction experiments per abstract (0.9) and the highest coverage of strains (92) and scientific articles (813). We compared methods that evaluate functional interactions among proteins (such as genomic context or co-expression) which are implemented in the STRING database. Most of these methods discriminate well between functionally relevant protein interactions (MPI-LIT) and high-throughput data.


BACKGROUND
http://www.jcvi.org/mpidb/interaction.php?dbsource=MPI-LIT.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Rajagopala
Seesandra V
SV
J Craig Venter Institute, Rockville, MD 20850, USA. raja@jcvi.org
Goll
Johannes
J
Gowda
N D Deve
ND
Sunil
Kumar C
KC
Titz
Björn
B
Mukherjee
Arnab
A
Mary
Sharmila S
SS
Raviswaran
Naresh
N
Poojari
Chetan S
CS
Ramachandra
Srinivas
S
Shtivelband
Svetlana
S
Blazie
Stephen M
SM
Hofmann
Julia
J
Uetz
Peter
P
D001426:Bacterial Proteins / Q000378:metabolism*; D019295:Computational Biology; D030562:Databases, Protein; D011485:Protein Binding; D025941:Protein Interaction Mapping
D001426:Bacterial Proteins
Nucleic Acids Res. 2007 Jan;35(Database issue):D572-4
17135203
Mol Syst Biol. 2007;3:128
17667950
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D418-24
15608229
Genome Res. 2003 Oct;13(10):2363-71
14525934
Nature. 1989 Jul 20;340(6230):245-6
2547163
BMC Bioinformatics. 2006 Jul 26;7:360
16872496
Nature. 2004 Jul 1;430(6995):88-93
15190252
Nucleic Acids Res. 2001 Jan 1;29(1):123-5
11125067
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D449-51
14681454
PLoS Biol. 2007 Mar;5(3):e16
17355171
Trends Genet. 2002 Oct;18(10):529-36
12350343
BMC Biol. 2007 Oct 09;5:44
17925023
Nature. 2001 Jan 11;409(6817):211-5
11196647
Genome Biol. 2007;8(7):R130
17615063
Bioinformatics. 2006 Jul 1;22(13):1600-7
16606683
Nucleic Acids Res. 2008 Jan;36(Database issue):D190-5
18045787
Nature. 2005 Feb 3;433(7025):531-7
15690043
Bioinformatics. 2008 Aug 1;24(15):1743-4
18556668
PLoS One. 2008 May 28;3(5):e2292
18509523
Nucleic Acids Res. 2007 Jan;35(Database issue):D561-5
17145710
J Biol. 2006;5(4):11
16762047
Nucleic Acids Res. 2007 Jan;35(Database issue):D358-62
17098935
DNA Res. 2007 Oct 31;14(5):207-16
18000013
Bioinformatics. 2006 Jan 1;22(1):103-5
16267085
FEBS Lett. 2008 Apr 9;582(8):1178-81
18328824
Genome Res. 2006 May;16(5):686-91
16606699