This article is part of a special issue on epigenomics.

Open Access Research

Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity

Alok K Tewari1, Galip Gürkan Yardimci1, Yoichiro Shibata1, Nathan C Sheffield1, Lingyun Song1, Barry S Taylor3, Stoyan G Georgiev1, Gerhard A Coetzee45, Uwe Ohler167, Terrence S Furey8, Gregory E Crawford19 and Phillip G Febbo10112*

Author Affiliations

1 Institute for Genome Sciences & Policy, Duke University, Durham, NC 27708, USA

2 Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA 94115, USA

3 Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA

4 Department of Preventive Medicine, Norris Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA

5 Department of Urology, Norris Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA

6 Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27708, USA

7 Department of Computer Science, Duke University, Durham, NC 27708, USA

8 Departments of Biology and Genetics, Carolina Center for Genome Sciences and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA

9 Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA

10 Department of Medicine, University of California at San Francisco School of Medicine, San Francisco, CA 94115, USA

11 Department of Urology, University of California at San Francisco School of Medicine, San Francisco, CA 94115, USA

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Genome Biology 2012, 13:R88  doi:10.1186/gb-2012-13-10-r88

Published: 3 October 2012

Additional files

Additional file 1:

Supplemental information containing four supplemental figures and three supplemental tables.

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Additional file 2:

Table S4 detailing RefSeq genes identified as differentially expressed in response to androgen receptor activation by mRNA-seq. mRNA from three biological replicates of LNCaP and three biological replicates of LNCaP-induced was extracted and sequenced. Genes differentially regulated by AR activation were determined using edgeR at a threshold of FDR < 0.05.

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Additional file 3:

Table S5 showing a comparison of androgen receptor-regulated genes as determined by mRNA-seq to previously published androgen receptor-regulated gene lists. Genes identified as differentially regulated by AR activation are shown along with all other RefSeq genes, ranked in order by the number of published studies that identify the gene as AR-regulated.

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