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Updated: May 30, 2026

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
Published on: October 3, 2025
Restructuring the gene ontology to emphasise regulative pathways and to improve gene similarity queries
Alessia Visconti1, Roberto Esposito, Francesca Cordero
1Department of Computer Science, University of Torino, Corso Svizzera 185, 10049, Torino, Italy. visconti@di.unito.it
Abstract:
The Gene Ontology (GO) has been developed to provide a structured vocabulary for genes description. Conversely, gene functional similarity measures would benefit from a structure tailored to emphasise genes involved in the same biological context. Therefore, such measures often find it difficult to fully exploit the information in the GO. This paper reorganises the GO to emphasise regulative information thus providing a better structure for functional analysis. A gene functional similarity measure exploiting the new structure is proposed. Empirical evidence shows that the new structure correctly captures regulative processes and that it can be used to support the proposed measure.
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