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..
Related article
AtPID Database Statistics
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. Intuitive query interfaces of AtPID allow easy access to important features of proteins. It provides a wealth of information for systematic understanding of gene functions and biological processes through incorporating synthetic resources. It also provides extensive linkouts from our data pages to other Arabidopsis resources for deeper mining.
The current version of the Web : Version3.00 AtPID is subject to periodic updates. Therefore, do visit back on this page to get the latest associations whenever needed.
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: 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