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Correcting signal biases and detecting regulatory elements in STARR-seq data.

Publication ,  Journal Article
Kim, Y-S; Johnson, GD; Seo, J; Barrera, A; Cowart, TN; Majoros, WH; Ochoa, A; Allen, AS; Reddy, TE
Published in: Genome Res
May 2021

High-throughput reporter assays such as self-transcribing active regulatory region sequencing (STARR-seq) have made it possible to measure regulatory element activity across the entire human genome at once. The resulting data, however, present substantial analytical challenges. Here, we identify technical biases that explain most of the variance in STARR-seq data. We then develop a statistical model to correct those biases and to improve detection of regulatory elements. This approach substantially improves precision and recall over current methods, improves detection of both activating and repressive regulatory elements, and controls for false discoveries despite strong local correlations in signal.

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Published In

Genome Res

DOI

EISSN

1549-5469

Publication Date

May 2021

Volume

31

Issue

5

Start / End Page

877 / 889

Location

United States

Related Subject Headings

  • Humans
  • High-Throughput Nucleotide Sequencing
  • Genome, Human
  • Enhancer Elements, Genetic
  • Bioinformatics
  • Bias
  • 3105 Genetics
  • 11 Medical and Health Sciences
  • 06 Biological Sciences
 

Citation

APA
Chicago
ICMJE
MLA
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Kim, Y.-S., Johnson, G. D., Seo, J., Barrera, A., Cowart, T. N., Majoros, W. H., … Reddy, T. E. (2021). Correcting signal biases and detecting regulatory elements in STARR-seq data. Genome Res, 31(5), 877–889. https://doi.org/10.1101/gr.269209.120
Kim, Young-Sook, Graham D. Johnson, Jungkyun Seo, Alejandro Barrera, Thomas N. Cowart, William H. Majoros, Alejandro Ochoa, Andrew S. Allen, and Timothy E. Reddy. “Correcting signal biases and detecting regulatory elements in STARR-seq data.Genome Res 31, no. 5 (May 2021): 877–89. https://doi.org/10.1101/gr.269209.120.
Kim Y-S, Johnson GD, Seo J, Barrera A, Cowart TN, Majoros WH, et al. Correcting signal biases and detecting regulatory elements in STARR-seq data. Genome Res. 2021 May;31(5):877–89.
Kim, Young-Sook, et al. “Correcting signal biases and detecting regulatory elements in STARR-seq data.Genome Res, vol. 31, no. 5, May 2021, pp. 877–89. Pubmed, doi:10.1101/gr.269209.120.
Kim Y-S, Johnson GD, Seo J, Barrera A, Cowart TN, Majoros WH, Ochoa A, Allen AS, Reddy TE. Correcting signal biases and detecting regulatory elements in STARR-seq data. Genome Res. 2021 May;31(5):877–889.

Published In

Genome Res

DOI

EISSN

1549-5469

Publication Date

May 2021

Volume

31

Issue

5

Start / End Page

877 / 889

Location

United States

Related Subject Headings

  • Humans
  • High-Throughput Nucleotide Sequencing
  • Genome, Human
  • Enhancer Elements, Genetic
  • Bioinformatics
  • Bias
  • 3105 Genetics
  • 11 Medical and Health Sciences
  • 06 Biological Sciences