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Cited by 112Genomics and Chromatin DynamicsChromatin Remodeling and CancerGenomics and Phylogenetic Studies

Accurate prediction of cell type-specific transcription factor binding

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Keilwagen, Jens, Posch, Stefan, Grau, Jan·2019·Genome Biology
DOI 10.1186/s13059-018-1614-yPMC PMC6327544
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Abstract

Prediction of cell type-specific, in vivo transcription factor binding sites is one of the central challenges in regulatory genomics. Here, we present our approach that earned a shared first rank in the "ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge" in 2017. In post-challenge analyses, we benchmark the influence of different feature sets and find that chromatin accessibility and binding motifs are sufficient to yield state-of-the-art performance. Finally, we provide 682 lists of predicted peaks for a total of 31 transcription factors in 22 primary cell types and tissues and a user-friendly version of our approach, Catchitt, for download.

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  • Prior work has shown minimal variation in performance between chromosomes on the ENCODE problem, so training and test distributions can be approximated as identical.

    “Prior work has shown that there is minimal variation in performance between chromosomes on this problem (Won et al., 2010; Alipanahi et al., 2015; Keilwagen et al., 2019), so we can approximate these training and test distributions as identical.”

    From WILDS: A Benchmark of in-the-Wild Distribution Shifts (2020) · cites this paper as Keilwagen et al., 2019

    The Results section says the ENCODE-DREAM predictions were evaluated on held-out chromosomes chr1, chr8, and chr21, but it does not compare performance between chromosomes. Searches for chromosome-level performance variation and training–test distribution similarity found no passage establishing minimal variation. The cited paper therefore does not verify the premise attributed to it. (LLM, conf=0.72)

    Experimental — accuracy not yet measured

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References 68 · Cited by 112

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Authors
Keilwagen, J., Posch, S., & Grau, J.
Affiliations
  • Julius Kühn-Institut (DE)
  • Martin Luther University Halle-Wittenberg (DE)
Corresponding author
Grau, Jan
ORCID
Venue
Genome Biology
Publisher
Springer Science and Business Media LLC
Published
2019-01-10
Volume
20
Issue
1
Pages
9-9
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
DOI
10.1186/s13059-018-1614-y
PMC
PMC6327544
OpenAlex
W2912321349
Cited by
112
References
68
Citations by year
2026: 3 · 2025: 9 · 2024: 13 · 2023: 8 · 2022: 21 · 2021: 29 · 2020: 21 · 2019: 5 · 2018: 3
FWCI
6.28
Type
journal article
Language
en
Open access
Licence
Locations
  • Genome biology (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • OpenAgrar (submittedVersion, cc-by)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
transcription factor binding site prediction, cell type-specific binding, chromatin accessibility, binding motifs, regulatory genomics, feature set comparison
MeSH terms
Cells, Humans, Transcription Factors, Genomics

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