Enhancer transcripts mark active estrogen receptor binding sites
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Cites methods from "Enhancer transcripts mark active es..."
...Using ChIA-PET, a correlation is revealed between expression level of elncRNAs and estrogen receptor a (ERa)-associated chromatin interactions [72]....
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"Enhancer transcripts mark active es..." refers methods in this paper
...The raw files were aligned to hg18 using BOWTIE (Langmead et al. 2009)....
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"Enhancer transcripts mark active es..." refers methods in this paper
...…et al. (Kraus) April 16, 2013 14 To determine which transcription factors might underlie the predicted enhancers identified based on the called transcripts from GRO-seq, we performed de novo motif analyses on a 1 kb region around the center of the eRNA overlap using MEME (Bailey et al. 2009)....
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...De novo motif searching was performed on a 1 kb region around the center of the plus and minus strand overlap (+/- 500 bp) using the command-line version of MEME (Bailey and Elkan 1994)....
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...Cold Spring Harbor Laboratory Press on October 3, 2014 - Published by genome.cshlp.orgDownloaded from Hah et al. (Kraus) April 16, 2013 14 To determine which transcription factors might underlie the predicted enhancers identified based on the called transcripts from GRO-seq, we performed de novo motif analyses on a 1 kb region around the center of the eRNA overlap using MEME (Bailey et al. 2009)....
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...De novo motif searching was performed on a 1 kb region around the center of the plus and minus strand overlap (+/- 500 bp) using MEME....
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...The predicted motifs from MEME were matched to known motifs using STAMP (Parks and Beiko 2010)....
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4,978 citations
"Enhancer transcripts mark active es..." refers methods in this paper
...De novo motif searching was performed on a 1 kb region around the center of the plus and minus strand overlap (+/- 500 bp) using the command-line version of MEME (Bailey and Elkan 1994)....
[...]
...Cold Spring Harbor Laboratory Press on October 3, 2014 - Published by genome.cshlp.orgDownloaded from Hah et al. (Kraus) April 16, 2013 14 To determine which transcription factors might underlie the predicted enhancers identified based on the called transcripts from GRO-seq, we performed de novo motif analyses on a 1 kb region around the center of the eRNA overlap using MEME (Bailey et al. 2009)....
[...]
...De novo motif searching was performed on a 1 kb region around the center of the plus and minus strand overlap (+/- 500 bp) using MEME....
[...]
...The predicted motifs from MEME were matched to known motifs using STAMP (Parks and Beiko 2010)....
[...]
...The predicted motifs from MEME were then matched to known motifs using STAMP (Parks and Beiko 2010)....
[...]
4,450 citations
"Enhancer transcripts mark active es..." refers methods in this paper
...…II transcription, and the production of enhancer RNAs Cold Spring Harbor Laboratory Press on October 3, 2014 - Published by genome.cshlp.orgDownloaded from Hah et al. (Kraus) April 16, 2013 4 (“eRNAs”) (De Santa et al. 2010; Kim et al. 2010; Hah et al. 2011; Wang et al. 2011; Djebali et al. 2012)....
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