REEF: searching REgionally Enriched Features in genomes

Abstract

Background: In Eukaryotic genomes, different features including genes are not uniformly distributed. The integration of annotation information and genomic position of functional DNA elements in the Eukaryotic genomes opened the way to test novel hypotheses of higher order genome organization and regulation of expression.

Results: REEF is a new tool, aimed at identifying genomic regions enriched in specific features, such as a class or group of genes homogeneous for expression and/or functional characteristics. The method for the calculation of local feature enrichment uses test statistic based on the Hypergeometric Distribution applied genome-wide by using a sliding window approach and adopting the False Discovery Rate for controlling multiplicity. REEF software, source code and documentation are freely available at http://telethon.bio.unipd.it/bioinfo/reef/.

Conclusion: REEF can aid to shed light on the role of organization of specific genomic regions in the determination of their functional role.

Figure 1

Screenshot of REEF genome view. In the main panel, the positions along human chromosomes of 44 clusters of at least 3 tissue-specific genes are shown; the navigating bar at the left allows to display selected chromosomes or clusters, whereas the bottom panel contains a genomic summary about data and results.

Figure 2

REEF chromosome plot and cluster view. In the chromosome plot at the top of the figure, the enrichment in tissue-specific genes along chromosome 1 is represented by plotting the quantity 1 - p-value for subsequent windows considered on the DNA sequence. The value corresponding to the sixth cluster is shown in red and a summary of analyzed data and results for the selected cluster is given below the plot, along with a link to the view in the UCSC Genome Browser of the cluster region with custom annotation tracks. The cluster view is shown in the bottom part of the figure.