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PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways.

Huaiyu Mi1, Nan Guo, Anish Kejariwal

  • 1Evolutionary Systems Biology Group, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA.

Nucleic Acids Research
|November 30, 2006
PubMed
Summary
This summary is machine-generated.

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The PANTHER system now links protein sequence evolution to function using improved evolutionary trees and expanded pathway data. This enhances understanding of biological roles across organisms.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • The Protein ANalysis THrough Evolutionary Relationships (PANTHER) system has been a key resource for understanding protein evolution and function since 2005.
  • Previous versions focused on protein families and gene ontology annotations.

Purpose of the Study:

  • To detail significant updates to the PANTHER system, enhancing its capabilities for analyzing protein evolution and function.
  • To highlight the integration of new data and methodologies for a more comprehensive understanding of biological roles.

Main Methods:

  • Selection of diverse protein sequences for robust phylogenetic and functional information in evolutionary trees.
  • Integration of PANTHER Hidden Markov Models (HMMs) into the InterProScan resource for broader accessibility.

Related Experiment Videos

  • Expansion of PANTHER pathways using Systems Biology Markup Language (SBML) and CellDesigner, with expert curation.

    • Main Results:

    • Improved evolutionary trees provide better phylogenetic and functional insights.
    • PANTHER HMMs are now accessible via InterProScan, increasing their utility.
    • A significantly expanded collection of approximately 1500 reactions in 130 curated pathways offers detailed functional context.

    Conclusions:

    • The updated PANTHER system offers a more powerful and integrated approach to studying protein evolution and function.
    • The expanded pathway data, linked to HMMs, enables inference of reactions across diverse organisms.
    • Continued development and expert curation ensure PANTHER remains a valuable resource for biological research.