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Discovery of active enhancers through bidirectional expression of short transcripts

Michael F Melgar1,2, Francis S Collins1* and Praveen Sethupathy3,4,5*

1 Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA

2 Current address: School of Medicine, The University of California at San Francisco, 505 Parnassus Avenue, San Francisco, CA 94143, USA

3 Department of Genetics, The University of North Carolina at Chapel Hill, 130 South Building, Chapel Hill, NC 27599, USA

4 Carolina Center for Genome Sciences, The University of North Carolina at Chapel Hill, 130 South Building, Chapel Hill, NC 27599, USA

5 Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, 130 South Building, Chapel Hill, NC 27599, USA

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Genome Biology 2011, 12:R113 doi:10.1186/gb-2011-12-11-r113

Published: 14 November 2011

Additional files

Additional file 1:

Receiver operating characteristic (ROC) curve depicting the sensitivity and specificity at various IMR90 GRO-seq read density cutoffs for gene activity. This figure shows that a cutoff of 5 reads/kb/mapability achieves the best combination of sensitivity and specificity, according to the maximal accuracy metric.

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Additional file 2:

Inverse correlation between promoter-proximal pausing index and level of gene transcription in IMR90 cells. This figure shows that promoter-proximal pausing of RNA polymerase is high for lowly expressed genes and low for highly expressed genes.

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Additional file 3:

Representation of BEST at three different enhancer subtypes in mouse embryonic stem cells. This figure shows that signal for BEST (bidirectional expression of short transcripts) is approximately two-fold and approximately eight-fold enriched at strong enhancers relative to weak enhancers and poised enhancers, respectively.

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