Deepm5C: A deep-learning-based hybrid framework for identifying human RNA N5-methylcytosine sites using a stacking strategy.
Mol Ther
; 30(8): 2856-2867, 2022 08 03.
Article
en En
| MEDLINE
| ID: mdl-35526094
ABSTRACT
As one of the most prevalent post-transcriptional epigenetic modifications, N5-methylcytosine (m5C) plays an essential role in various cellular processes and disease pathogenesis. Therefore, it is important accurately identify m5C modifications in order to gain a deeper understanding of cellular processes and other possible functional mechanisms. Although a few computational methods have been proposed, their respective models have been developed using small training datasets. Hence, their practical application is quite limited in genome-wide detection. To overcome the existing limitations, we propose Deepm5C, a bioinformatics method for identifying RNA m5C sites throughout the human genome. To develop Deepm5C, we constructed a novel benchmarking dataset and investigated a mixture of three conventional feature-encoding algorithms and a feature derived from word-embedding approaches. Afterward, four variants of deep-learning classifiers and four commonly used conventional classifiers were employed and trained with the four encodings, ultimately obtaining 32 baseline models. A stacking strategy is effectively utilized by integrating the predicted output of the optimal baseline models and trained with a one-dimensional (1D) convolutional neural network. As a result, the Deepm5C predictor achieved excellent performance during cross-validation with a Matthews correlation coefficient and an accuracy of 0.697 and 0.855, respectively. The corresponding metrics during the independent test were 0.691 and 0.852, respectively. Overall, Deepm5C achieved a more accurate and stable performance than the baseline models and significantly outperformed the existing predictors, demonstrating the effectiveness of our proposed hybrid framework. Furthermore, Deepm5C is expected to assist community-wide efforts in identifying putative m5Cs and to formulate the novel testable biological hypothesis.
Palabras clave
Texto completo:
1
Banco de datos:
MEDLINE
Asunto principal:
ARN
/
Aprendizaje Profundo
Tipo de estudio:
Prognostic_studies
Límite:
Humans
Idioma:
En
Revista:
Mol Ther
Asunto de la revista:
BIOLOGIA MOLECULAR
/
TERAPEUTICA
Año:
2022
Tipo del documento:
Article