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The Proteome Browser - A Software Resource for the Chromosome-Centric Human Proteome Project

posted May 2, 2013, 9:09 PM by TPB Administrator   [ updated May 5, 2013, 6:08 PM ]
The Proteome Browser is a web-based portal to the human proteome developed to support the efforts of the Australian/New Zealand consortium in the Chromosome-centric Human Proteome Project (C-HPP). This portal, built in conjunction with the Proteomics community, includes a data integration and analysis software system that integrates up-to-date pertinent information from multiple large international biological databases that house genomic and protein data, and assembles this information into a format suitable for a global proteomics effort of the kind proposed by the C-HPP.

The Proteome Browser integrates protein data from a number of source systems including Ensemble, GPM, The Human Protein Atlas and NeXtProt. The data collections from this portal are also made discoverable through ANDS' Research Data Australia.

The Proteome Browser provides a web interface that is designed to display an overview of the current evidence supporting the identification of various gene products across the chromosome, such as protein expression, modification and disease association, with the ability to drill down to the original data. The design of the portal allows for easy addition of both new data sources and data categories.

The ‘traffic light’ representation of proteomic data, includes an X axis that relates to each gene (i.e. protein) ordered by default in the order found on the Chromosome, and the Y axis relates to the types of evidence that support the identification of proteins. The traffic light system is used to indicate cases where different types of data exists or do not exist for a particular protein.

Various aspects of the underlying contributing information are available for further analyses using clustering and drill down/through capabilities. The user interface is dynamic, showing relevant information by providing the ability to filter; and also provides links to external systems where appropriate.

The Proteome Browser has produced significant benefits for Australian and international proteomic researchers by:
  • Providing an extendable platform to support mining of new and existing proteomics data for novel research outcomes
  • Supporting the C-HPP initiative by providing a visualisation tool for the ‘Trans Proteomic Pipeline’, the standard analysis pipeline for proteomic data
  • Enabling researchers to identify all predicted proteins and their isoforms, followed by cataloguing and analysis of the associated data
  • Enabling the integration of data from different sources to provide a cohesive view of the existing proteomic landscape which includes
    • Creating a portal to the human proteome
    • Delineating the complex proteome in the context of the linear genome
    • Enabling comprehensive analysis by supporting the interrogation of multiple genes simultaneously
    • Providing a measure of data confidence
  • Facilitating the linking of data into a common research data space, through the Australian Research Data Commons.