Informative databases and useful search tools tested and recommended by Jen Sheen (5/23/2010)


Arabidopsis Interactions Viewer
http://bar.utoronto.ca/interactions/cgi-bin/arabidopsis_interactions_viewer.cgi

The Arabidopsis Interactions Viewer queries a database of 70944 predicted and 4300 confirmed Arabidopsis interacting proteins. The predicted interactions (interologs) were generated by Drs. Matt Geisler and Jane Geisler-Lee (Geisler-Lee et al., 2007) at the Southern Illinois University. Their current version is Interactome 2.0. The confirmed Arabidopsis interacting proteins come from BIND, the Biomolecular Interaction Network Database, high-density Arabidopsis protein microarrays (Popescu et al, 2007; Popescu et al., 2009) and other literature sources. The interactions in BIND were identified using several different methods, such as yeast two hybrid screens, but also via traditional biochemical methods. Use the links to BIND/PubMed records that are in the output of this viewer to view further information. All subcellular localisation data is from SUBA, the Arabidopsis Subcellular Database. These localizations do not include predicted localizations.

Important References
Jane Geisler-Lee, Nicholas O’Toole, Ron Ammar, Nicholas J. Provart, A. Harvey Millar, and Matt Geisler. A Predicted Interactome for Arabidopsis. Plant Physiology, October 2007, Vol. 145, pp. 317–329

Popescu SC, Popescu GV, Bachan S, Zhang Z, Seay M, Gerstein M, Snyder M, Dinesh-Kumar SP. Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays. Proc Natl Acad Sci   U S A. 2007, Mar 13;104(11):4730-4735.

Sorina C. Popescu, George V. Popescu, Shawn Bachan, Zimei Zhang, Mark Gerstein, Michael Snyder & Savithramma P. Dinesh-Kumar. MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays. Genes Dev. 2009 23:80-92

ATPIN
http://bioinfo.esalq.usp.br/atpin/atpin.pl

AtPINDB integrates more than 96,000 PPIs (96,221 as in release 8) from five public available databases: IntAct, BIOGRID, Arabidopsis protein-protein interaction data curated from the literature by TAIR curators, the Predicted Interactome for Arabidopsis, and the A. thaliana Protein Interactome Database (AtPID). All of the databases are queried weekly for updates.

Marcelo M Brandao, Luiza L Dantas and Marcio C Silva-Filho. AtPIN: Arabidopsis thaliana Protein Interaction Network. BMC Bioinformatics 2009, 10:454

ATPID
http://atpid.biosino.org/

This database includes 28,062 protein-protein interaction pairs involving 12,506 proteins with 23,396 pairs from prediction methods, while the other 4,666 pairs involving 2,285 proteins are manually curated from literatures. In addition, subcellular localizations of 5,562 proteins are also included.

Jian Cui, Peng Li, Guang Li, Feng Xu, Chen Zhao, Yuhua Li, Zhongnan Yang, Guang Wang, Qingbo Yu, Yixue Li and Tieliu Shi. AtPID: Arabidopsis thaliana protein interactome database—an integrative platform for plant systems biology.
Nucleic Acids Research, 2008, Vol. 36, Database issue D999–D1008


Arabidopsis Membrane Interactome Project
http://www.associomics.org/search.php

AMPv2: pilot screen with 445 Nub and 206 Cub clones -- total 362 interactions found (Lalonde et al. manuscript in preparation).
AMPv3: large-scale screen with 2288 Nub and 1421 Cub clones -- total 102,232 interactions found (Lalonde & Frommer, unpublished).

Disclaimer: While AMPv2 has been carefully quality-controlled, AMPv3 is based on a 'quick and dirty' image analysis (500uM methionine) with arbitrarily set cut-offs. The aim of this analysis was to provide the community with potential leads for interactions for their favorite genes (absolutely no warranty). You can check the corresponding images in the database. The dataset will contain a large number of false positive and negative data; none of the interactions has been verified independently, nor have we checked whether known interactions are present in the database! Each gene should have been tested in duplicate, but there may be plates missing (e.g. due to contamination). We will update the database once we completed the careful image and statistical analysis for 0 and 500uM methionine, and we expect to add new data for AMPv4 in June/July. AMPv4 that will lead to a total coverage of 3800x2400 interaction pairs.

CORNET
http://bioinformatics.psb.ugent.be/cornet/
https://bioinformatics.psb.ugent.be/cornet/main/ppi

This is a very useful site covering many databases. The amount of data alone makes it worth checking out.

Stefanie De Bodt, Diana Carvajal, Jens Hollunder, Joost Van den Cruyce, Sara Movahedi, and Dirk Inze. CORNET: A User-Friendly Tool for Data Mining and Integration. Plant Physiology, March 2010, Vol. 152, pp. 1167–1179