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 4.0
Protein interactions involve in important cellular functions and biological processes, and is the fundamentals of all life activities. With the research technique improvement and the research progresses, the overall protein interaction network frameworks of several model organisms have been set up through data collection and integration. However, most of such networks being processed only behold simple relationships without border weight or direction, so that it is far from the biological reality. In vivo, different types of protein interaction, such as the assembly of protein complexes, phosphorylation or immune recognition, often has its specific functions and qualifications. Ignorance of these features will bring much bias to the network analysis and application. Therefore, We annotate the protein with further information (e.g., functional annotation, subcellular localization, tissue-specific expression, SNP phenotype, and mutant phenotype , etc.) and interaction qualifications (e.g.,transcriptional regulation, complex assembly, (de)phosphorylation, functional collaboration, etc.) via literature text mining and integration of other resources, meanwhile, the related information is comprehensively and vivid displayed to the user through the newly developed display and analytical tools.
The current version of the Web : Version4.00 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