Genome-wide prediction of transcription factor binding sites using an integrated model
Open accessAbstract
We present an integrated method called Chromia for the genome-wide identification of functional target loci of transcription factors. Designed to capture the characteristic patterns of transcription factor binding motif occurrences and the histone profiles associated with regulatory elements such as promoters and enhancers, Chromia significantly outperforms other methods in the identification of 13 transcription factor binding sites in mouse embryonic stem cells, evaluated by both binding (ChIP-seq) and functional (RNA interference knockdown) experiments.
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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 Won et al., 2010
The Results section, “Leave-one-chromosome-out cross-validation” (page unavailable), says that each chromosome was held out for testing in turn, but does not report whether performance varied minimally between chromosomes. The passages found on chromosome-wise performance also do not establish that the training and test distributions were identical; the paper’s evaluation described here used mouse embryonic stem-cell data. (LLM, conf=0.72)
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- Authors
- Won, K.-J., Ren, B., & Wang, W.
- Affiliations
- University of California San Diego (US)
- Ludwig Cancer Research (BE)
- Corresponding author
- Wang, Wei
- Venue
- Genome Biology
- Published
- 2010-01-22
- Volume
- 11
- Issue
- 1
- Pages
- R7-R7
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC2847719
- OpenAlex
- W2078034709
- Cited by
- 116
- References
- 58
- Citations by year
- 2026: 2 · 2024: 1 · 2023: 4 · 2022: 2 · 2021: 6 · 2020: 4 · 2019: 4 · 2018: 4 · 2017: 3 · 2016: 5 · 2015: 13 · 2014: 10 · 2013: 19 · 2012: 12
- FWCI
- 7.56
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Institutes of Health
- National Institute of General Medical Sciences (R01GM072856)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- transcription factor binding sites, chromia, regulatory elements, promoter, enhancers, mouse embryonic stem cells, ChIP-seq, RNAi knockdown, genomic prediction
- MeSH terms
- Animals, Binding Sites, Chromatin, Enhancer Elements, Genetic, Models, Genetic, Promoter Regions, Genetic, ROC Curve, Transcription Factors, Genome, Computational Biology, Amino Acid Motifs, RNA Interference, Chromatin Immunoprecipitation, Mice, Embryonic Stem Cells
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