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ORIGINAL RESEARCH article

Front. Genet.

Sec. Computational Genomics

Volume 16 - 2025 | doi: 10.3389/fgene.2025.1684484

This article is part of the Research TopicGenomic Medicine, Therapeutics, and Health: Thai Symposium & Workshop in BangkokView all articles

CGSDA: Inferring snoRNA-disease associations via ChebNetII and GatedGCN

Provisionally accepted
Yongfu  ZouYongfu Zou1Yusong  LuYusong Lu1*Shanghui  LuShanghui Lu1Zhanliang  WeiZhanliang Wei2Le  LiLe Li3Shuilin  LiaoShuilin Liao4Ting  ZengTing Zeng4Yi  ZhangYi Zhang5Miao  RuiMiao Rui3
  • 1Hechi University, Hechi, China
  • 2The Second Nanning People's Hospital, Nanning, China
  • 3Zunyi Medical University - Zhuhai Campus, Zhuhai, China
  • 4Macau University of Science and Technology, Macau, China
  • 5Nanning Normal University, Nanning, China

The final, formatted version of the article will be published soon.

Recent biomedical studies have highlighted the pivotal role of non-coding RNAs (ncRNAs) in gene regulatory networks, where they influence gene expression, cellular function, and the onset and progression of various diseases. Among these, small nucleolar RNAs (snoRNAs), a prominent class of small ncRNAs, have attracted considerable research attention over the past two decades. Initially recognized for their involvement in rRNA processing and modification, snoRNAs are now understood to contribute to broader biological processes, including the regulation of disease mechanisms, maintenance of cellular homeostasis, and development of targeted therapeutic strategies. With ongoing advancements, snoRNAs are increasingly regarded as promising candidates for novel therapeutic agents in cancer, neurodegenerative disorders, endocrine conditions, and cardiovascular diseases. Consequently, there is a growing demand for efficient, cost-effective, and environment-independent approaches to study snoRNAs, which has driven the adoption of computational methodologies in this domain. In this work, we propose a novel predictive framework, CGSDA, which integrates a ChebNetII convolutional network with a gated graph sequence neural network to identify potential snoRNA–disease associations. The model begins by constructing a snoRNA–disease association network, embedding residual mechanisms into both modules to effectively capture the representations of snoRNAs and diseases. These representations are then fused and dimensionally reduced, after which the refined embeddings are fed into a predictor to generate association predictions. Experimental evaluation demonstrates that CGSDA consistently outperforms baseline models in predictive accuracy. Ablation experiments were conducted to assess the contribution of each module, confirming that all components substantially enhance overall performance and validating the robustness of the proposed method. Furthermore, case studies on lung cancer and breast cancer showed that 10 out of the top 15 and 12 out of the top 15 predicted snoRNA-disease associations Zou et al. SDA prediction by CGSDA were validated by existing literature, respectively, confirming the model's effectiveness in identifying potential novel snoRNA-disease associations. The implementation of CGSDA, along with relevant datasets, is publicly available at: https://github.com/cuntjx/CGSDA.

Keywords: Disease-snoRNA association, GNNS, ChebNetII Convolutional Network, Gated Graph Convolutional Network, Multiplefeatures fusion, Residual Mechanism

Received: 13 Aug 2025; Accepted: 06 Oct 2025.

Copyright: © 2025 Zou, Lu, Lu, Wei, Li, Liao, Zeng, Zhang and Rui. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Yusong Lu, luyusongky@163.com

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