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Original Article Issue
Compound toxicity prediction based on transcriptomics data and gene ontology knowledge
Military Medical Sciences 2025, 49(3): 178-184
Published: 25 March 2025
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Objective

To develop a new model for predicting compound toxicity and exploring related toxicity mechanisms using transcriptomic data and gene ontology knowledge.

Methods

Using the TOXRIC database, two toxicity-related datasets were constructed and a Tox VNN model was established that incorporated gene ontology knowledge to evaluate compound toxicity and identify key biological processes.

Results

Tox VNN demonstrated good predictability. The identification of important biological processes related to CYP enzyme activity and p53 pathway stress response provided insights into the toxicity mechanisms.

Conclusion

The Tox VNN, which integrates data and knowledge, can not only ensure high predictability, but also effectively identify important biological processes related to toxicity. This model offers a new approach to predicting and understanding compound toxicity in drug safety evaluation.

Regular Paper Issue
Synthetic Lethal Interactions Prediction Based on Multiple Similarity Measures Fusion
Journal of Computer Science and Technology 2021, 36(2): 261-275
Published: 05 March 2021
Abstract Collect

The synthetic lethality (SL) relationship arises when a combination of deficiencies in two genes leads to cell death, whereas a deficiency in either one of the two genes does not. The survival of the mutant tumor cells depends on the SL partners of the mutant gene, thereby the cancer cells could be selectively killed by inhibiting the SL partners of the oncogenic genes but normal cells could not. Therefore, there is an urgent need to develop more efficient computational methods of SL pairs identification for cancer targeted therapy. In this paper, we propose a new approach based on similarity fusion to predict SL pairs. Multiple types of gene similarity measures are integrated and k-nearest neighbors algorithm (k-NN) is applied to achieve the similarity-based classification task between gene pairs. As a similarity-based method, our method demonstrated excellent performance in multiple experiments. Besides the effectiveness of our method, the ease of use and expansibility can also make our method more widely used in practice.

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