{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,21]],"date-time":"2026-03-21T19:23:58Z","timestamp":1774121038043,"version":"3.50.1"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2025,9,8]],"date-time":"2025-09-08T00:00:00Z","timestamp":1757289600000},"content-version":"vor","delay-in-days":7,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"France G\u00e9nomique National infrastructure"},{"name":"Investissements d\u2019Avenir\u201d program managed by the Agence Nationale de la Recherche","award":["ANR-10-INBS-09"],"award-info":[{"award-number":["ANR-10-INBS-09"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Graph neural network (GNN) models have emerged in many fields and notably for biological networks constituted by genes or proteins and their interactions. The majority of enrichment study methods apply over-representation analysis and gene\/protein set scores according to the existing overlap between pathways. Such methods neglect knowledges coming from the interactions between the gene\/protein sets. Here, we introduce a novel GNN-based enrichment analysis method called GNNenrich. GNNenrich, through multiple levels of embedding that integrate protein sequence properties and interactions network, establishes functional relationship to support biological interpretation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>GNNenrich have been tested and compared to over-representation analysis technique (g:Profiler) and graph-based method (EnrichNet). It demonstrates the capacity to reproduce results provided by others approaches and offers new perspectives for interpretation, returning relevant results supported by protein\u2013protein interactions (PPIs).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Source code is available at https:\/\/gitlab.com\/cnrgh\/gnn-enrich\/gnn-enrich-article-demo.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf478","type":"journal-article","created":{"date-parts":[[2025,9,8]],"date-time":"2025-09-08T15:13:06Z","timestamp":1757344386000},"source":"Crossref","is-referenced-by-count":2,"title":["GNNenrich: a novel method for pathway enrichment analysis based on graph neural network"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8324-0891","authenticated-orcid":false,"given":"Mallek","family":"Mziou-Sallami","sequence":"first","affiliation":[{"name":"Centre National de Recherche en G\u00e9nomique Humaine, Institut Fran\u00e7ois Jacob CEA Universit\u00e9 Paris-Saclay , \u00c9vry-Courcouronnes 91000,","place":["France"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8177-4873","authenticated-orcid":false,"given":"Pierrick","family":"Roger","sequence":"additional","affiliation":[{"name":"Centre National de Recherche en G\u00e9nomique Humaine, Institut Fran\u00e7ois Jacob CEA Universit\u00e9 Paris-Saclay , \u00c9vry-Courcouronnes 91000,","place":["France"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-9141-3406","authenticated-orcid":false,"given":"Arnaud","family":"Gloaguen","sequence":"additional","affiliation":[{"name":"Centre National de Recherche en G\u00e9nomique Humaine, Institut Fran\u00e7ois Jacob CEA Universit\u00e9 Paris-Saclay , \u00c9vry-Courcouronnes 91000,","place":["France"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3340-2001","authenticated-orcid":false,"given":"Claire","family":"Dandine-Roulland","sequence":"additional","affiliation":[{"name":"Centre National de Recherche en G\u00e9nomique Humaine, Institut Fran\u00e7ois Jacob CEA Universit\u00e9 Paris-Saclay , \u00c9vry-Courcouronnes 91000,","place":["France"]}]},{"given":"Thierry","family":"Jiogho Ngaho","sequence":"additional","affiliation":[{"name":"Centre National de Recherche en G\u00e9nomique Humaine, Institut Fran\u00e7ois Jacob CEA Universit\u00e9 Paris-Saclay , \u00c9vry-Courcouronnes 91000,","place":["France"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0209-5467","authenticated-orcid":false,"given":"Sol\u00e8ne","family":"Brohard","sequence":"additional","affiliation":[{"name":"Centre National de Recherche en G\u00e9nomique Humaine, Institut Fran\u00e7ois Jacob CEA Universit\u00e9 Paris-Saclay , \u00c9vry-Courcouronnes 91000,","place":["France"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3988-7772","authenticated-orcid":false,"given":"K\u00e9vin","family":"Muret","sequence":"additional","affiliation":[{"name":"Centre National de Recherche en G\u00e9nomique Humaine, Institut Fran\u00e7ois Jacob CEA Universit\u00e9 Paris-Saclay , \u00c9vry-Courcouronnes 91000,","place":["France"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7491-0283","authenticated-orcid":false,"given":"Florian","family":"Sandron","sequence":"additional","affiliation":[{"name":"Centre National de Recherche en G\u00e9nomique Humaine, Institut Fran\u00e7ois Jacob CEA Universit\u00e9 Paris-Saclay , \u00c9vry-Courcouronnes 91000,","place":["France"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8468-2867","authenticated-orcid":false,"given":"Eric","family":"Bonnet","sequence":"additional","affiliation":[{"name":"Centre National de Recherche en G\u00e9nomique Humaine, Institut Fran\u00e7ois Jacob CEA Universit\u00e9 Paris-Saclay , 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