Bioinformatics Primers

Pathway Interaction Database provides reviews and commentary illuminating topics of particular interest.

April 2009

• An Introduction to the PANTHER Pathway Resource

  

  PANTHER Pathway (http://www.pantherdb.org/pathway/), a module of the PANTHER Protein Classification System, was designed to model evolutionary sequence - function relationships on a large scale. The PANTHER Pathway database has several aims:
  1.  To comprehensively represent authored, "review-level" biological knowledge concerning both metabolic and signaling pathways, capturing mechanistic detail about each pathway step and literature evidence whenever possible
  2.  To provide clear visualization of pathways geared to biologist end users and genomic data-analysis tools that employ visualization
  3.  To provide structured pathway data for systems biology and bioinformatics analysis
  4.  To represent the evolution of each pathway, thus enabling accurate inferences across homologous genes and pathways in different model organisms

  Currently, PANTHER Pathway contains 165 expert-curated metabolic and signaling pathways, comprising 2985 reactions, 20,851 proteins directly associated to the pathways with an evidence code, and 3569 distinct literature references. All pathways were created with CellDesigner, a pathway editing tool that captures data in Systems Biology Markup Language (SBML) format and displays the pathway diagram in Systems Biology Graphical Notation (SBGN). Finally, PANTHER Pathway is supported by a number of PANTHER web tools, including the protein classification tool and gene expression analysis tool.

  Original research paper Pathway Interaction Database doi:10.1038/pid.2009.1