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AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology.

Cui J, Li P, Li G, Xu F, Zhao C, Li Y, Yang Z, Wang G, Yu Q, Li Y, Shi T - Nucleic Acids Res. (2007)

Bottom Line: Among the rest 4666 pairs, 3866 pairs of them involving 1875 proteins were manually curated from the literature and 800 pairs were from enzyme complexes in KEGG.In addition, subcellular location information of 5562 proteins is available.AtPID was built via an intuitive query interface that provides easy access to the important features of proteins.

View Article: PubMed Central - PubMed

Affiliation: College of Life Sciences, the Northeast Forestry University, Harbin, Heilongjiang 150040, China.

ABSTRACT
Arabidopsis thaliana Protein Interactome Database (AtPID) is an object database that integrates data from several bioinformatics prediction methods and manually collected information from the literature. It contains data relevant to protein-protein interaction, protein subcellular location, ortholog maps, domain attributes and gene regulation. The predicted protein interaction data were obtained from ortholog interactome, microarray profiles, GO annotation, and conserved domain and genome contexts. This database holds 28,062 protein-protein interaction pairs with 23,396 pairs generated from prediction methods. Among the rest 4666 pairs, 3866 pairs of them involving 1875 proteins were manually curated from the literature and 800 pairs were from enzyme complexes in KEGG. In addition, subcellular location information of 5562 proteins is available. AtPID was built via an intuitive query interface that provides easy access to the important features of proteins. Through the incorporation of both experimental and computational methods, AtPID is a rich source of information for system-level understanding of gene function and biological processes in A. thaliana. Public access to the AtPID database is available at http://atpid.biosino.org/.

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The AtPID interface of PPI Simple Search Results for the queried protein, HAP3A. There are generally three tables: (1) protein attributes with gene model descriptions and PPI summary, showing how many protein pairs can be predicted and the inferred interactions overlapped with GSP. (2) The second table represents interactants of the queried protein, HAP3A. Users can view what the experimental evidence is to support this consequence and link to corresponding literature(s). (3) The third table represents potential interactants of the queried protein, HAP3A, by Naïve Bays integration across the seven approaches. Each approach is graphically represented by circles. When the cursor is over a circle, it will display the corresponding score (LR) for the method.
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Figure 3: The AtPID interface of PPI Simple Search Results for the queried protein, HAP3A. There are generally three tables: (1) protein attributes with gene model descriptions and PPI summary, showing how many protein pairs can be predicted and the inferred interactions overlapped with GSP. (2) The second table represents interactants of the queried protein, HAP3A. Users can view what the experimental evidence is to support this consequence and link to corresponding literature(s). (3) The third table represents potential interactants of the queried protein, HAP3A, by Naïve Bays integration across the seven approaches. Each approach is graphically represented by circles. When the cursor is over a circle, it will display the corresponding score (LR) for the method.

Mentions: PPI query is the main function of AtPID, which makes available manually collected PPI data and predicted PPI through integrated data resources. Query flow is illustrated in Figure 2 and demonstrates how querying a protein name or protein pair on the query page accesses PPI information (http://atpid.biosino.org/query.php). AtPID allows several types of query keywords used by other databases, including UniProtKB/Swiss-Prot ID, TAIR AGI, Entrez Gene name, REFSEQ PROVISIONAL ID (NCBI) or International Protein Index (IPI) symbols. We defined three types of submissions. (i) ‘Simple search’ allows the user to submit a single protein. This search is appropriate when the user would like to know which other protein(s) have the highest probability of interacting with the protein of interest. The search results include the GSP and PPI predictions. (ii) ‘Pair search’ allows the user to submit a protein pair to ascertain if an interaction between two proteins has been documented. (iii) ‘Multiple search’ allows a user to query more than two proteins. A comma separate format is required to access an interaction network among multiple proteins. All returned pages inform the user of related protein annotations by text and graphs. For example, the user is interested in the HAP3A protein, which encodes a subunit of the CCAAT-binding complex and binds to the CCAAT box motif present in some plant promoter sequences. The ‘Search Results’ show a summary of the protein attributes in the first table, including the ‘Locus’, gene/protein symbol, the number of interactions (six from GSP and seven by inference), function description and database cross-references to Entrez, TAIR, IPI, UniProtKB/TrEMBL, UniParc and KEGG (Figure 3).Figure 2.


AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology.

Cui J, Li P, Li G, Xu F, Zhao C, Li Y, Yang Z, Wang G, Yu Q, Li Y, Shi T - Nucleic Acids Res. (2007)

The AtPID interface of PPI Simple Search Results for the queried protein, HAP3A. There are generally three tables: (1) protein attributes with gene model descriptions and PPI summary, showing how many protein pairs can be predicted and the inferred interactions overlapped with GSP. (2) The second table represents interactants of the queried protein, HAP3A. Users can view what the experimental evidence is to support this consequence and link to corresponding literature(s). (3) The third table represents potential interactants of the queried protein, HAP3A, by Naïve Bays integration across the seven approaches. Each approach is graphically represented by circles. When the cursor is over a circle, it will display the corresponding score (LR) for the method.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238993&req=5

Figure 3: The AtPID interface of PPI Simple Search Results for the queried protein, HAP3A. There are generally three tables: (1) protein attributes with gene model descriptions and PPI summary, showing how many protein pairs can be predicted and the inferred interactions overlapped with GSP. (2) The second table represents interactants of the queried protein, HAP3A. Users can view what the experimental evidence is to support this consequence and link to corresponding literature(s). (3) The third table represents potential interactants of the queried protein, HAP3A, by Naïve Bays integration across the seven approaches. Each approach is graphically represented by circles. When the cursor is over a circle, it will display the corresponding score (LR) for the method.
Mentions: PPI query is the main function of AtPID, which makes available manually collected PPI data and predicted PPI through integrated data resources. Query flow is illustrated in Figure 2 and demonstrates how querying a protein name or protein pair on the query page accesses PPI information (http://atpid.biosino.org/query.php). AtPID allows several types of query keywords used by other databases, including UniProtKB/Swiss-Prot ID, TAIR AGI, Entrez Gene name, REFSEQ PROVISIONAL ID (NCBI) or International Protein Index (IPI) symbols. We defined three types of submissions. (i) ‘Simple search’ allows the user to submit a single protein. This search is appropriate when the user would like to know which other protein(s) have the highest probability of interacting with the protein of interest. The search results include the GSP and PPI predictions. (ii) ‘Pair search’ allows the user to submit a protein pair to ascertain if an interaction between two proteins has been documented. (iii) ‘Multiple search’ allows a user to query more than two proteins. A comma separate format is required to access an interaction network among multiple proteins. All returned pages inform the user of related protein annotations by text and graphs. For example, the user is interested in the HAP3A protein, which encodes a subunit of the CCAAT-binding complex and binds to the CCAAT box motif present in some plant promoter sequences. The ‘Search Results’ show a summary of the protein attributes in the first table, including the ‘Locus’, gene/protein symbol, the number of interactions (six from GSP and seven by inference), function description and database cross-references to Entrez, TAIR, IPI, UniProtKB/TrEMBL, UniParc and KEGG (Figure 3).Figure 2.

Bottom Line: Among the rest 4666 pairs, 3866 pairs of them involving 1875 proteins were manually curated from the literature and 800 pairs were from enzyme complexes in KEGG.In addition, subcellular location information of 5562 proteins is available.AtPID was built via an intuitive query interface that provides easy access to the important features of proteins.

View Article: PubMed Central - PubMed

Affiliation: College of Life Sciences, the Northeast Forestry University, Harbin, Heilongjiang 150040, China.

ABSTRACT
Arabidopsis thaliana Protein Interactome Database (AtPID) is an object database that integrates data from several bioinformatics prediction methods and manually collected information from the literature. It contains data relevant to protein-protein interaction, protein subcellular location, ortholog maps, domain attributes and gene regulation. The predicted protein interaction data were obtained from ortholog interactome, microarray profiles, GO annotation, and conserved domain and genome contexts. This database holds 28,062 protein-protein interaction pairs with 23,396 pairs generated from prediction methods. Among the rest 4666 pairs, 3866 pairs of them involving 1875 proteins were manually curated from the literature and 800 pairs were from enzyme complexes in KEGG. In addition, subcellular location information of 5562 proteins is available. AtPID was built via an intuitive query interface that provides easy access to the important features of proteins. Through the incorporation of both experimental and computational methods, AtPID is a rich source of information for system-level understanding of gene function and biological processes in A. thaliana. Public access to the AtPID database is available at http://atpid.biosino.org/.

Show MeSH
Related in: MedlinePlus