PANTHER Protein Classification System Database 5.0

PANTHER, a protein classification system from Applied Biosystems, got updated to version 5.0. Proteins are classified by family, molecular and biological function (GO ontology) and known pathways. Its main use is probably microarray analysis - it incorporate automated GO surrepresentation analysis with graphical output. Best of all, its available freely. A paper describing the Database is available freely in the Nucleic acids research Journal.

Applied Biosystems (NYSE:ABI), an Applera Corporation business, today announced the latest release of the PANTHER™ system database of protein families, subfamilies, functions and pathways. Enhancements to the latest version, Panther 5.0, include interactive resources for associating protein families with their biological pathways, as well as new tools for analyzing gene expression data in relation to molecular functions, biological processes, and pathways. The PANTHER system database is publicly available without restriction at http://panther.appliedbiosystems.com. Today’s announcement coincides with the publication of a peer-reviewed paper describing the latest version of the PANTHER system database in the January 2005 edition of Nucleic Acids Research. In conjunction with this publication, PANTHER system will become part of the European Bioinformatics Institute’s InterPro database beginning in February, which provides an integrated view of the most commonly used protein databases through an intuitive interface for text- and sequence-based searches. “The PANTHER system provides scientists with a unique resource for gene function prediction and analysis based on a combination of advanced bioinformatics and manual data curation,” said Paul D. Thomas, Senior Director of Computational Biology for Applied Biosystems, Primary Investigator for the development of the PANTHER system, and lead author of the paper. “The significant enhancements in the latest version provide the scientific community with a wealth of freely available information and tools to advance systems biology. We are honored that the PANTHER system has been accepted as an InterPro member database and look forward to working with the community to further advance this resource.” The PANTHER system functional annotations of fruit fly genes have been available for two years as part of an ongoing collaboration with FlyBase. “The task of performing functional annotation of genomes is challenging. Too often we rely simply on transitive annotation based on a BLAST match. The PANTHER system offers a much more sophisticated system for predicting gene function from sequence,” said Michael Ashburner, Ph.D., Professor of Genetics at Cambridge University and a founder and co-principle investigator of FlyBase. “Our collaboration with the PANTHER system has been excellent and very informative for the annotation of the Drosophila genome.” This week’s release includes functional annotation information for human, mouse and rat genes in addition to the Drosophila genes. The PANTHER system database consists of a library of 6,683 protein families, divided into 31,750 functional subfamilies, and covering approximately 90% of mammalian protein coding genes. The Web-based interface allows life scientists to browse or analyze large sets of genes by their known or inferred biological functions and explore more than 60 pathways associated with protein families, subfamilies, and training sequences using diagrams drawn by expert curators. The new PANTHER system Pathway Module is the result of an ongoing collaboration with the Systems Biology Institute (SBI) in Tokyo, led by Dr. Hiroaki Kitano, a founding member of the SBML (Systems Biology Markup Language) Consortium. The CellDesigner software (http://www.celldesigner.org) developed by Dr. Kitano’s group was used to draw all of the pathways available on the PANTHER system Web site, which provides sufficient molecular detail of the pathway data for systems biology applications. “We've gained enormously from this collaboration, and we are pleased to be providing the results to the scientific community. Dr. Kitano’s ‘process notation’ is a key advance for representing biological pathways in a way that is accessible not only to bench biologists, but also to computational biologists. The CellDesigner software immensely simplifies the task of capturing and displaying detailed pathway data,” added Dr. Thomas. “This collaboration has been a terrific experience that has provided us with enormous feedback to improve the process notation and CellDesigner software. This is the first time that such a large set of pathway modules has been released with such detailed molecular information. We are pleased to see that the process notation in CellDesigner has proved to be scalable and practical,” said Dr. Kitano. “We congratulate the PANTHER system team for the contribution to the scientific community.” “The PANTHER system supports an integrated approach to protein and mRNA expression analysis with links to biological content, informatics tools, and lab instrumentation to support systems biology research,” said Dennis A. Gilbert, Ph.D., Chief Scientific Officer for Applied Biosystems. “Users can query the database using probe IDs from the Applied Biosystems Expression Array System to further characterize a gene of interest. Additionally, the PANTHER system workspace is integrated with the Applied Biosystems e-commerce site so users can order corresponding Applied Biosystems TaqMan® Gene Expression and SNP Genotyping Assays for further experimentation.” For more information about Panther 5.0 please visit http://panther.appliedbiosystems.com.

Source : Applied Biosystems Press Release