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Related Experiment Video

Updated: Jul 19, 2026

Pattern-based Search of Epigenomic Data Using GeNemo

Pattern-based Search of Epigenomic Data Using GeNemo

Published on: October 8, 2017

REEF: searching REgionally Enriched Features in genomes.

Alessandro Coppe¹, Gian Antonio Danieli, Stefania Bortoluzzi

¹Department of Biology, University of Padova, via G, Colombo 3, 35131, Padova, Italy. ale@telethon.bio.unipd.it

BMC Bioinformatics

|October 18, 2006

Summary

REEF identifies genomic regions with specific gene features. This tool helps understand how genome organization impacts gene function and regulation.

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Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Eukaryotic genomes exhibit non-uniform distribution of features like genes.
Integrating genomic position and annotation data enables novel hypotheses on genome organization and gene expression regulation.

Purpose of the Study:

To introduce REEF, a novel computational tool for identifying genomic regions enriched in specific features.
To facilitate the study of gene clusters with homogeneous expression or functional characteristics.

Main Methods:

Utilizes a sliding window approach across the genome.
Employs a test statistic based on the Hypergeometric Distribution for local feature enrichment calculation.
Applies the False Discovery Rate (FDR) for controlling multiplicity.

Main Results:

REEF identifies genomic regions exhibiting enrichment for specific gene classes or groups.
The tool is freely available with source code and documentation.

Conclusions:

REEF aids in elucidating the role of genomic region organization in determining functional roles.
Understanding spatial organization of genomic features is crucial for gene function.