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

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/.

• Publication year

  2010

• Venue

  Nucleic Acids Res.

• Publication date

  2010-10-29

• Fields of study

  Biology, Medicine, Computer Science, Environmental Science

• Identifiers
  DOI 10.1093/nar/gkq959PMID 21036873PMCID 3013798
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Conflict of interest statement. None declared.

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