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Related Experiment Videos

Exploring relationships and mining data with the UCSC Gene Sorter.

W J Kent1, Fan Hsu, Donna Karolchik

  • 1Howard Hughes Medical Institute, University of California, Santa Cruz, CA 95064, USA.

Genome Research
|May 4, 2005
PubMed
Summary

The UCSC Gene Sorter tool aids in studying gene function and evolution by graphically displaying and filtering related human genes. It offers customizable data views for comprehensive genomic exploration.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Human genome sequencing efforts have spurred the development of tools for gene set analysis.
  • Existing tools often focus on chromosomal organization, necessitating gene-centric approaches.

Purpose of the Study:

  • To introduce the UCSC Gene Sorter, a gene-centric tool for studying human gene function and evolution.
  • To provide a graphical interface for sorting and filtering gene sets based on diverse criteria.

Main Methods:

  • Development of a CGI-based web application using C and MySQL.
  • Integration with the UCSC Genome Browser suite for enhanced functionality.
  • Implementation of sorting and filtering capabilities based on expression, genomic proximity, Gene Ontology (GO) terms, and protein similarity.

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Main Results:

  • The UCSC Gene Sorter offers a graphical display of related genes.
  • Users can sort genes by expression profiles, genomic location, GO terms, and protein similarity.
  • Filtering options include expression levels, gene identifiers, and chromosomal positions.

Conclusions:

  • The UCSC Gene Sorter enhances interactive genomic exploration and analysis.
  • It serves as a valuable gene-based counterpart to chromosome-oriented browsers.
  • The tool facilitates in-depth study of gene function and evolutionary relationships.