Theory of methods
- Ortholog interaction datasets
- Shared biological function
- Co-expression matrices
- Gene fusion method
- Gene neighbors method
- Phylogenetic profile method
- Enriched domain pair
Bayesian Networks Approach
The Bayesian Networks approach was used to integrate the four predictive data sources and build a model to predict novel protein-protein interactions. More..
AtPID Database 5.0
AtPID (Arabidopsis thaliana Protein Interactome Database, available at http://www.megabionet.org/atpid) is an integrated database resource for protein interaction network and functional annotation. In the past few years, we collected 5,564 mutants with significant morphological alterations and manually curated them to 167 plant ontology (PO) morphology categories. These single/multiple-gene mutants were indexed and linked to 3,919 genes. After integrated these genotype-phenotype associations with the comprehensive protein interaction network in AtPID, we developed a Naïve Bayes method and predicted 4,457 novel high confidence gene-PO pairs with 1,369 genes as the complement. Along with the accumulated novel data for protein interaction and functional annotation, and the updated visualization toolkits, we present a genome-scale resource for genotype-phenotype associations in Arabidopsis, AtPID 5.0. In our updated website, all the new genotype-phenotype associations from mutants, protein network, and the protein annotation information could be vividly displayed in a comprehensive network view, which will greatly enhance plant protein function, and genotype-phenotype association studies in a systematical way.
The current version of the Web : Version 5.00 AtPID is subject to periodic updates.
What 's new?
The usefulness of AtPID
AtPID construct Arabidopsis Protein-protein interaction network and has capability of throughly topological analysis to the certain pathway so that we could not only query the subcellular localizations, functional modules, protein annotations, but also enhance the understanding of proteomics of Arabidopsis comprehensively. We provide this website for two reasons: one is to facilitate biologists to design experiments flexibly through particular analysis according to our network. Another is to enrich the Arabidopsis golden standard positive/ negative datasets and correct the deviations and errors within our protein-protein network. Based on the above attempts, we can also enlarge the quantity and advance the quality of the data depository in AtPID by fabricating componentized, hierarchical and dynamic network of protein regulations utilizing the current plenty of microarray profiles under various tissues, stress treatments or during growing periods.
Please cite: Peng Li, Weidong Zang, Yuhua Li, Feng Xu, Jigang Wang, and Tieliu Shi. AtPID: the overall hierarchical functional protein interaction network interface and analytic platform for Arabidopsis Nucl. Acids Res. (2011) 39 (suppl 1): D1130-D1133. doi: 10.1093/nar/gkq959