Identifying new cancer genes based on the integration of annotated gene sets via hypergraph neural networks.
Bioinformatics
; 40(Supplement_1): i511-i520, 2024 Jun 28.
Article
in En
| MEDLINE
| ID: mdl-38940121
ABSTRACT
MOTIVATION Identifying cancer genes remains a significant challenge in cancer genomics research. Annotated gene sets encode functional associations among multiple genes, and cancer genes have been shown to cluster in hallmark signaling pathways and biological processes. The knowledge of annotated gene sets is critical for discovering cancer genes but remains to be fully exploited. RESULTS:
Here, we present the DIsease-Specific Hypergraph neural network (DISHyper), a hypergraph-based computational method that integrates the knowledge from multiple types of annotated gene sets to predict cancer genes. First, our benchmark results demonstrate that DISHyper outperforms the existing state-of-the-art methods and highlight the advantages of employing hypergraphs for representing annotated gene sets. Second, we validate the accuracy of DISHyper-predicted cancer genes using functional validation results and multiple independent functional genomics data. Third, our model predicts 44 novel cancer genes, and subsequent analysis shows their significant associations with multiple types of cancers. Overall, our study provides a new perspective for discovering cancer genes and reveals previously undiscovered cancer genes. AVAILABILITY AND IMPLEMENTATION DISHyper is freely available for download at https//github.com/genemine/DISHyper.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Neural Networks, Computer
/
Neoplasms
Limits:
Humans
Language:
En
Journal:
Bioinformatics
Journal subject:
INFORMATICA MEDICA
Year:
2024
Type:
Article
Affiliation country:
China