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
Transcriptional regulation and mutant phenotype are especially critical for protein function study in plants. Although great efforts have been made on collecting related data in plants, the mutant phenotype and transcriptional regulation are still largely under-annotated, with only 10.3% and 15.4% of genome annotated in Arabidopsis. The low genome coverage in annotation makes systematical analyses hard to be undertaken. In addition, the disperse data in different resources are not well integrated and not fully utilized. Therefore, we integrated known data and predicted genome-wide candidates for transcriptional regulation and mutant phenotype in the updated AtPID. Specifically, we extended the original mutant-phenotypes by supplementing 3,663 known ones extracted from databases and literatures and 4,457 novel ones from computational prediction. We also predicted 31,991 and 143,691 transcriptional regulations of 6,891 and 15,302 genes with high and low confidence respectively, considerably extending the genome coverage by 46.0%. These updated data can be accessed through a friendly interface. This updated AtPID will greatly enhance protein function studies in a systematical way for Arabidopsis.
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