Modulation of DNA-protein Interactions by Proximal Genetic Elements as Uncovered by Interpretable Deep Learning

Kalakoti, Yogesh; Peter, Swathik Clarancia; Gawande, Swaraj; Sundar, Durai

doi:10.1016/j.jmb.2023.168121

Cited by 3 publications

(2 citation statements)

References 44 publications

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“…TL was utilized to predict the TF and DNA motif binding by Kalakoti et al (2023) [ 79 ]. Their method to investigate the binding of TF and DNA sequences was K-mer-based and included 26 different TF.…”

Section: Gene Expressionmentioning

confidence: 99%

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Transfer Learning in Cancer Genetics, Mutation Detection, Gene Expression Analysis, and Syndrome Recognition

Ashayeri,

Sobhi,

Pławiak

et al. 2024

Cancers

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Artificial intelligence (AI), encompassing machine learning (ML) and deep learning (DL), has revolutionized medical research, facilitating advancements in drug discovery and cancer diagnosis. ML identifies patterns in data, while DL employs neural networks for intricate processing. Predictive modeling challenges, such as data labeling, are addressed by transfer learning (TL), leveraging pre-existing models for faster training. TL shows potential in genetic research, improving tasks like gene expression analysis, mutation detection, genetic syndrome recognition, and genotype–phenotype association. This review explores the role of TL in overcoming challenges in mutation detection, genetic syndrome detection, gene expression, or phenotype–genotype association. TL has shown effectiveness in various aspects of genetic research. TL enhances the accuracy and efficiency of mutation detection, aiding in the identification of genetic abnormalities. TL can improve the diagnostic accuracy of syndrome-related genetic patterns. Moreover, TL plays a crucial role in gene expression analysis in order to accurately predict gene expression levels and their interactions. Additionally, TL enhances phenotype–genotype association studies by leveraging pre-trained models. In conclusion, TL enhances AI efficiency by improving mutation prediction, gene expression analysis, and genetic syndrome detection. Future studies should focus on increasing domain similarities, expanding databases, and incorporating clinical data for better predictions.

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Section: Gene Expressionmentioning

confidence: 99%

“…Their method to investigate the binding of TF and DNA sequences was K-mer-based and included 26 different TF. With this model, they achieved an accuracy of 95.6% [ 79 ]. Histopathologic images of cancer are also a good source for gene expression and predicting their response to the therapy.…”

Section: Gene Expressionmentioning

confidence: 99%