AtPID: the overall hierarchical functional protein interaction network interface and analytic platform for Arabidopsis

Abstract

Protein interactions are involved in important cellular functions and biological processes that are the fundamentals of all life activities. With improvements in experimental techniques and progress in research, the overall protein interaction network frameworks of several model organisms have been created through data collection and integration. However, most of the networks processed only show simple relationships without boundary, weight or direction, which do not truly reflect the biological reality. In vivo, different types of protein interactions, such as the assembly of protein complexes or phosphorylation, often have their specific functions and qualifications. Ignorance of these features will bring much bias to the network analysis and application. Therefore, we annotate the Arabidopsis proteins in the AtPID database with further information (e.g. functional annotation, subcellular localization, tissue-specific expression, phosphorylation information, SNP phenotype and mutant phenotype, etc.) and interaction qualifications (e.g. transcriptional regulation, complex assembly, functional collaboration, etc.) via further literature text mining and integration of other resources. Meanwhile, the related information is vividly displayed to users through a comprehensive and newly developed display and analytical tools. The system allows the construction of tissue-specific interaction networks with display of canonical pathways. The latest updated AtPID database is available at http://www.megabionet.org/atpid/.

Figure 1.

Protein–protein interaction network display. Edges color: red, PPI with evidence; green, proteins in small complex; blue, transcriptional regulation. Vertices color: green, gene with mutant info; purple, genes with selected subcellular localization info; Dark green, genes with selected pathway info; blue, shortest path starting and ending protein; black, shortest path via protein. Vertices shape: regular pentagon, phosphoproteins; 5-pointed star, proteins with selected tissue information. (A) Node right menu. (B) Node mouse hovering annotation.