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Wiki-Pi: A Web-Server of Annotated Human Protein-Protein Interactions to Aid in Discovery of Protein Function
Abstract Protein-protein interactions (PPIs) are thProtein-protein interactions (PPIs) are the basis of biological functions. Knowledge of the interactions of a protein can help understand its molecular function and its association with different biological processes and pathways. Several publicly available databases provide comprehensive information about individual proteins, such as their sequence, structure, and function. There also exist databases that are built exclusively to provide PPIs by curating them from published literature. The information provided in these web resources is protein-centric, and not PPI-centric. The PPIs are typically provided as lists of interactions of a given gene with links to interacting partners; they do not present a comprehensive view of the nature of both the proteins involved in the interactions. A web database that allows search and retrieval based on biomedical characteristics of PPIs is lacking, and is needed. We present Wiki-Pi (read Wiki-π), a web-based interface to a database of human PPIs, which allows users to retrieve interactions by their biomedical attributes such as their association to diseases, pathways, drugs and biological functions. Each retrieved PPI is shown with annotations of both of the participant proteins side-by-side, creating a basis to hypothesize the biological function facilitated by the interaction. Conceptually, it is a search engine for PPIs analogous to PubMed for scientific literature. Its usefulness in generating novel scientific hypotheses is demonstrated through the study of IGSF21, a little-known gene that was recently identified to be associated with diabetic retinopathy. Using Wiki-Pi, we infer that its association to diabetic retinopathy may be mediated through its interactions with the genes HSPB1, KRAS, TMSB4X and DGKD, and that it may be involved in cellular response to external stimuli, cytoskeletal organization and regulation of molecular activity. The website also provides a wiki-like capability allowing users to describe or discuss an interaction. Wiki-Pi is available publicly and freely at http://severus.dbmi.pitt.edu/wiki-pi/. at http://severus.dbmi.pitt.edu/wiki-pi/.
Abstractsub Protein-protein interactions (PPIs) are thProtein-protein interactions (PPIs) are the basis of biological functions. Knowledge of the interactions of a protein can help understand its molecular function and its association with different biological processes and pathways. Several publicly available databases provide comprehensive information about individual proteins, such as their sequence, structure, and function. There also exist databases that are built exclusively to provide PPIs by curating them from published literature. The information provided in these web resources is protein-centric, and not PPI-centric. The PPIs are typically provided as lists of interactions of a given gene with links to interacting partners; they do not present a comprehensive view of the nature of both the proteins involved in the interactions. A web database that allows search and retrieval based on biomedical characteristics of PPIs is lacking, and is needed. We present Wiki-Pi (read Wiki-π), a web-based interface to a database of human PPIs, which allows users to retrieve interactions by their biomedical attributes such as their association to diseases, pathways, drugs and biological functions. Each retrieved PPI is shown with annotations of both of the participant proteins side-by-side, creating a basis to hypothesize the biological function facilitated by the interaction. Conceptually, it is a search engine for PPIs analogous to PubMed for scientific literature. Its usefulness in generating novel scientific hypotheses is demonstrated through the study of IGSF21, a little-known gene that was recently identified to be associated with diabetic retinopathy. Using Wiki-Pi, we infer that its association to diabetic retinopathy may be mediated through its interactions with the genes HSPB1, KRAS, TMSB4X and DGKD, and that it may be involved in cellular response to external stimuli, cytoskeletal organization and regulation of molecular activity. The website also provides a wiki-like capability allowing users to describe or discuss an interaction. Wiki-Pi is available publicly and freely at http://severus.dbmi.pitt.edu/wiki-pi/. at http://severus.dbmi.pitt.edu/wiki-pi/.
Bibtextype article  +
Doi 10.1371/journal.pone.0049029  +
Has author Orii N. + , Ganapathiraju M.K. +
Has extra keyword Drug + , Amino acid sequence + , Article + , Biological functions + , Biomedicine + , Cell activity + , Cell stimulation + , Computer interface + , Computer program + , Cytoskeleton + , DGKD gene + , Diabetic retinopathy + , Disease association + , Gene + , Genetic association + , HSPB1 gene + , Human + , IGFS21 gene + , Information retrieval + , KRAS gene + , Protein analysis + , Protein database + , Protein function + , Protein protein interaction + , Protein structure + , Regulatory mechanism + , Signal transduction + , TMSB4X gene + , Databases + , Protein + , Humans + , Internet + , Protein Interaction Mapping + , Search Engine + , Tool +
Issn 19326203  +
Issue 11  +
Language English +
Number of citations by publication 0  +
Number of references by publication 0  +
Published in PLoS ONE +
Pubmed 23209562  +
Title Wiki-Pi: A Web-Server of Annotated Human Protein-Protein Interactions to Aid in Discovery of Protein Function +
Type journal article  +
Volume 7  +
Year 2012 +
Creation dateThis property is a special property in this wiki. 8 November 2014 07:39:34  +
Categories Publications without keywords parameter  + , Publications without license parameter  + , Publications without remote mirror parameter  + , Publications without archive mirror parameter  + , Publications without paywall mirror parameter  + , Journal articles  + , Publications without references parameter  + , Publications  +
Modification dateThis property is a special property in this wiki. 8 November 2014 07:39:34  +
DateThis property is a special property in this wiki. 2012  +
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Wiki-Pi: A Web-Server of Annotated Human Protein-Protein Interactions to Aid in Discovery of Protein Function + Title
 

 

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