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Kerfuffle: a web tool for multi-species gene colocalization analysis.

Robert Aboukhalil1, Bernard Fendler, Gurinder S Atwal

  • 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA. raboukha@cshl.edu

BMC Bioinformatics
|January 19, 2013
PubMed
Summary

Kerfuffle is a new web tool that helps researchers study gene colocalization across many species. It aids in understanding genome organization and evolutionary pressures by visualizing and quantifying gene clusters.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Eukaryotic genome organization and evolutionary pressures remain poorly understood.
  • Functionally similar genes may cluster in genomes, indicating chromatin-level gene regulation.
  • Existing bioinformatic tools lack systematic, multi-species gene colocalization analysis capabilities.

Purpose of the Study:

  • To develop a novel bioinformatic tool for multi-species gene colocalization analysis.
  • To facilitate the discovery, visualization, and quantification of conserved gene clusters across diverse species.
  • To aid in understanding genome functional organization and evolutionary relationships.

Main Methods:

  • Kerfuffle web tool queries Ensembl BioMart for gene positional and homology information.
  • Performs multi-species clustering analysis on user-specified human genes and selected species.
  • Utilizes Monte Carlo simulations for statistical significance and Circos software for visualization.

Main Results:

  • Kerfuffle identifies and quantifies significant gene colocalization across up to 47 species.
  • Provides downloadable lists of clustered genes and estimates cluster conservation.
  • Generates interactive graphs and visualizations of gene cluster organization.

Conclusions:

  • Kerfuffle is an easy-to-use, publicly available tool for functional and comparative genomics.
  • Enables flexible, rapid investigation of gene clusters and their evolutionary significance.
  • Results can be saved for further analysis, aiding in the exploration of enriched molecular pathways.