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.
机构:Tokyo Med & Dent Univ, Sch Biomed Sci, Dept Biosyst Modeling, Tokyo, Japan
Fukuoka, Y
;
Inaoka, H
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Tokyo Med & Dent Univ, Sch Biomed Sci, Dept Biosyst Modeling, Tokyo, JapanTokyo Med & Dent Univ, Sch Biomed Sci, Dept Biosyst Modeling, Tokyo, Japan
Inaoka, H
;
Kohane, IS
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机构:Tokyo Med & Dent Univ, Sch Biomed Sci, Dept Biosyst Modeling, Tokyo, Japan
机构:Tokyo Med & Dent Univ, Sch Biomed Sci, Dept Biosyst Modeling, Tokyo, Japan
Fukuoka, Y
;
Inaoka, H
论文数: 0引用数: 0
h-index: 0
机构:
Tokyo Med & Dent Univ, Sch Biomed Sci, Dept Biosyst Modeling, Tokyo, JapanTokyo Med & Dent Univ, Sch Biomed Sci, Dept Biosyst Modeling, Tokyo, Japan
Inaoka, H
;
Kohane, IS
论文数: 0引用数: 0
h-index: 0
机构:Tokyo Med & Dent Univ, Sch Biomed Sci, Dept Biosyst Modeling, Tokyo, Japan