PuSH - Publication Server of Helmholtz Zentrum München: DeepLocRNA: An interpretable deep learning model for predicting RNA subcellular localisation with domain-specific transfer-learning.

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Wang, J.* ; Horlacher, M. ; Cheng, L.* ; Winther, O.*

DeepLocRNA: An interpretable deep learning model for predicting RNA subcellular localisation with domain-specific transfer-learning.

Bioinformatics 40:btae065 (2024)

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MOTIVATION: Accurate prediction of RNA subcellular localisation plays an important role in understanding cellular processes and functions. Although post-transcriptional processes are governed by trans-acting RNA binding proteins (RBPs) through interaction with cis-regulatory RNA motifs, current methods do not incorporate RBP-binding information. RESULTS: In this paper, we propose DeepLocRNA, an interpretable deep-learning model that leverages a pre-trained multi-task RBP-binding prediction model to predict the subcellular localisation of RNA molecules via fine-tuning. We constructed DeepLocRNA using a comprehensive dataset with variant RNA types and evaluated it on the held-out dataset. Our model achieved state-of-the-art performance in predicting RNA subcellular localisation in mRNA and miRNA. It has also demonstrated great generalization capabilities, performing well on both human and mouse RNA. Additionally, a motif analysis was performed to enhance the interpretability of the model, highlighting signal factors that contributed to the predictions. The proposed model provides general and powerful prediction abilities for different RNA types and species, offering valuable insights into the localisation patterns of RNA molecules and contributing to our understanding of cellular processes at the molecular level. A user-friendly web server is available at: https://biolib.com/KU/DeepLocRNA/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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