The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data - PubMed (original) (raw)
The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data
H Ramos et al. Bioinformatics. 2008.
Abstract
Motivation: Mass spectrometry experiments in the field of proteomics produce lists containing tens to thousands of identified proteins. With the protein information and property explorer (PIPE), the biologist can acquire functional annotations for these proteins and explore the enrichment of the list, or fraction thereof, with respect to functional classes. These protein lists may be saved for access at a later time or different location. The PIPE is interoperable with the Firegoose and the Gaggle, permitting wide-ranging data exploration and analysis. The PIPE is a rich-client web application which uses AJAX capabilities provided by the Google Web Toolkit, and server-side data storage using Hibernate.
Availability: http://pipe.systemsbiology.net.
Figures
Fig. 1.
(A) Through the Firegoose, the PIPE and the Gaggle interchange data at the click of the ‘Broadcast’ button. (B) Logging into the PIPE produces a view summarizing all previously entered datasets. (C) Opening a dataset produces a view of the data and a menu bar containing operations which can be performed on the data. Here, we have performed an ID Mapping operation from IPI numbers to Entrez Gene ID, gene symbol and description. (D) When no mapping is found for a protein identifier, clicking on the ‘na’ value gives the user the option to lookup the protein sequence or enter the missing value. (E) The results of a GO enrichment operation are presented in a Gaggled Cytoscape window (Shannon et al., 2003, 2006).
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