Motivation: Gene regulation involves complex interactions between transcription factors. While early attempts to predict gene expression were trained using naturally occurring promoters, gigantic parallel reporter assays have vastly expanded potential training data. Despite this, it is still unclear how to best use deep learning to study gene regulation. Here, we investigate the association between promoters and expression using Camformer, a residual convolutional neural network that ranked fourth in the Random Promoter DREAM Challenge 2022. We present the original model trained on 6.7 million sequences and investigate 270 alternative models to find determinants of model performance. Finally, we use explainable AI to uncover regulatory signals.
Results: Camformer accurately decodes the association between promoters and gene expression (
Availability and implementation: Data and code are available at: https://github.com/Bornelov-lab/Camformer.
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Evidence ID | Analyze ID | Gene/Complex | Systematic Name/Complex Accession | Qualifier | Gene Ontology Term ID | Gene Ontology Term | Aspect | Annotation Extension | Evidence | Method | Source | Assigned On | Reference |
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Evidence ID | Analyze ID | Gene | Gene Systematic Name | Phenotype | Experiment Type | Experiment Type Category | Mutant Information | Strain Background | Chemical | Details | Reference |
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Evidence ID | Analyze ID | Gene | Gene Systematic Name | Disease Ontology Term | Disease Ontology Term ID | Qualifier | Evidence | Method | Source | Assigned On | Reference |
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Evidence ID | Analyze ID | Regulator | Regulator Systematic Name | Target | Target Systematic Name | Direction | Regulation of | Happens During | Regulator Type | Direction | Regulation Of | Happens During | Method | Evidence | Strain Background | Reference |
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Site | Modification | Modifier | Source | Reference |
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Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Allele | Assay | Annotation | Action | Phenotype | SGA score | P-value | Source | Reference | Note |
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Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Assay | Annotation | Action | Modification | Source | Reference | Note |
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Complement ID | Locus ID | Gene | Species | Gene ID | Strain background | Direction | Details | Source | Reference |
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Evidence ID | Analyze ID | Dataset | Description | Keywords | Number of Conditions | Reference |
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Evidence ID | Analyze ID | File | Description |
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