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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

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Large-scale gene function analysis with the PANTHER classification system.

Huaiyu Mi1, Anushya Muruganujan, John T Casagrande

  • 1Department of Preventive Medicine, Division of Bioinformatics, Keck School of Medicine, University of Southern California, Los Angeles, California, USA. huaiyumi@usc.edu

Nature Protocols
|July 23, 2013
PubMed
Summary
This summary is machine-generated.

The PANTHER classification system offers comprehensive tools for analyzing large-scale genomic data. Its updated interface and expanded data enhance gene function, pathway, and evolutionary relationship analysis for biologists.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • The PANTHER (Protein ANnotation THrough Evolutionary Relationships) classification system integrates gene function, ontology, and pathway data.
  • It utilizes 82 complete genomes, phylogenetic trees, and hidden Markov models (HMMs) to capture evolutionary relationships.
  • Existing tools facilitate analysis of large-scale genomic data from sequencing, proteomics, and gene expression experiments.

Purpose of the Study:

  • To provide a detailed protocol for analyzing genome-wide experimental data using the PANTHER classification system.
  • To describe the features and capabilities of the PANTHER system, including its data content and analytical tools.
  • To highlight improvements in the 2013 release (v.8.0), focusing on website interface redesign and enhanced analytical capabilities.

Main Methods:

  • Utilizing the PANTHER classification system, which organizes genes into families and subfamilies based on evolutionary relationships.
  • Annotating genes with Gene Ontology (GO) and PANTHER protein class terms.
  • Assigning gene sequences to PANTHER pathways and employing statistical tests for data analysis.

Main Results:

  • The PANTHER system provides a robust framework for classifying gene function and analyzing evolutionary relationships.
  • The 2013 release (v.8.0) features an updated data content and a redesigned website interface for improved user experience.
  • The system's analytical capabilities have been enhanced, supporting a wide range of statistical tests for large-scale data analysis.

Conclusions:

  • The PANTHER classification system is a valuable resource for biologists, bioinformaticians, and systems biologists for analyzing complex genomic datasets.
  • The updated system offers improved usability and analytical power for exploring gene function, pathways, and evolutionary contexts.
  • This protocol serves as a guide for effectively leveraging PANTHER's capabilities in modern biological research.