CREaTor: zero-shot cis-regulatory pattern modeling with attention mechanisms
Open accessPublished version of a preprint
Abstract
Linking cis -regulatory sequences to target genes has been a long-standing challenge. In this study, we introduce CREaTor, an attention-based deep neural network designed to model cis -regulatory patterns for genomic elements up to 2 Mb from target genes. Coupled with a training strategy that predicts gene expression from flanking candidate cis -regulatory elements (cCREs), CREaTor can model cell type-specific cis -regulatory patterns in new cell types without prior knowledge of cCRE-gene interactions or additional training. The zero-shot modeling capability, combined with the use of only RNA-seq and ChIP-seq data, allows for the ready generalization of CREaTor to a broad range of cell types.
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References 57 · Cited by 12
- Authors
- Li, Y., Ju, F., Chen, Z., Qu, Y., Xia, H., He, L., Wu, L., Zhu, J., Shao, B., & Deng, P.
- Affiliations
- Microsoft Research Asia (China) (CN)
- Australian National University (AU)
- Corresponding author
- Deng, Pan
- Venue
- Genome Biology
- Published
- 2023-11-23
- Volume
- 24
- Issue
- 1
- Pages
- 266-266
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC10666311
- OpenAlex
- W4388929106
- Cited by
- 12
- References
- 57
- Citations by year
- 2026: 4 · 2025: 3 · 2024: 3 · 2023: 2
- FWCI
- 1.07
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- cis-regulatory elements, zero-shot learning, attention mechanism, deep neural network, gene expression prediction, cell type-specific gene regulation, creators, RNA-seq, ChIP-seq
- MeSH terms
- Regulatory Sequences, Nucleic Acid, Neural Networks, Computer
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