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Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

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A Web Tool for Generating High Quality Machine-readable Biological Pathways
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A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

PANTHER pathway: an ontology-based pathway database coupled with data analysis tools.

Huaiyu Mi1, Paul Thomas

  • 1Evolutionary Systems Biology Group, SRI International, Menlo Park, CA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|July 15, 2009
PubMed
Summary
This summary is machine-generated.

Systems biology research utilizes computational tools and pathway databases for data analysis. This chapter highlights the role of ontologies and standards, using PANTHER Pathway as an example, in biological knowledge representation and gene expression analysis.

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A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
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Area of Science:

  • Systems biology
  • Bioinformatics
  • Computational biology

Background:

  • The increasing availability of genomic data and experimental results necessitates advanced analytical approaches.
  • Computational tools and algorithms for biological pathway network analysis have significantly advanced research capabilities.
  • Pathway databases are crucial components of the systems biology research paradigm.

Purpose of the Study:

  • To discuss the representation of biological knowledge, emphasizing ontologies and standards in systems biology.
  • To illustrate the application of ontologies and standards in data modeling, entry, and display using PANTHER Pathway.
  • To describe the utilization of systems and computational tools for analyzing gene expression data.

Main Methods:

  • Review of biological knowledge representation methods, focusing on ontologies.
  • Case study of PANTHER Pathway to demonstrate the role of standards in data management.
  • Description of computational tools for analyzing gene expression data with pathway information.

Main Results:

  • Ontologies and standards are vital for organizing and integrating biological knowledge.
  • PANTHER Pathway effectively employs ontologies for structured data modeling, entry, and display.
  • Computational tools can leverage pathway information for insightful gene expression data analysis.

Conclusions:

  • Standardized representations like ontologies are fundamental for effective systems biology research.
  • PANTHER Pathway serves as a model for integrating biological data through standardized frameworks.
  • The described computational approaches facilitate deeper understanding of gene expression patterns within biological pathways.