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Although tomato molecular response to individual stresses is well studied, the gene regulatory network (GRN) representing the crosstalk and trade\u2010offs of multi\u2010stress responses remains almost unexplored.\n                        <\/jats:p>\n                      <\/jats:list-item>\n                      <jats:list-item>\n                        <jats:p>We developed GENIAL (Gene rEgulatory Network and topologIcal datA anaLysis) to refine and analyze complex GRNs and TomTom, a knowledge graph that gathers 11 publicly available databases in a unique FAIR (Findable, Accessible, Interoperable, Reproducible) resource. To test GENIAL, we used transcriptomics data from tomato subjected to six distinct pathogens from the literature.<\/jats:p>\n                      <\/jats:list-item>\n                      <jats:list-item>\n                        <jats:p>\n                          GENIAL yielded the identification of transcription factors (TFs) coordinating the specific and multiple pathogen response. Functional validation using the virus\u2010induced gene silencing system in tomato demonstrated that ETHYLENE RESPONSE FACTOR 16 and TCP DOMAIN PROTEIN 17 act as key TFs in the response to\n                          <jats:italic>Botrytis cinerea<\/jats:italic>\n                          , as silencing of either TF resulted in increased susceptibility. The validation of selected downstream targets allowed the validation of the robustness of the interactions highlighted by GENIAL.\n                        <\/jats:p>\n                      <\/jats:list-item>\n                      <jats:list-item>\n                        <jats:p>This study represents a proof of concept of our framework and can be extended to include other molecular layers and scaled to other questions involving tomato and beyond.<\/jats:p>\n                      <\/jats:list-item>\n                    <\/jats:list>\n                  <\/jats:p>","DOI":"10.1111\/nph.71382","type":"journal-article","created":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T03:20:06Z","timestamp":1782962406000},"page":"3039-3055","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["From knowledge graph to topological data analysis: a novel framework to analyze gene regulatory networks for tomato\u2013multi\u2010pathogen interactions"],"prefix":"10.1111","volume":"251","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-4704-3580","authenticated-orcid":false,"given":"Maxime","family":"Multari","sequence":"first","affiliation":[{"name":"INRAE, Universit\u00e9 C\u00f4te d'Azur, Institut Sophia Agrobiotech  06903 Sophia\u2010Antipolis France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9434-7392","authenticated-orcid":false,"given":"Mathieu","family":"Carri\u00e8re","sequence":"additional","affiliation":[{"name":"Data Shape Team, Centre Inria d'Universit\u00e9 C\u00f4te d'Azur  06903 Sophia\u2010Antipolis France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xavier","family":"Amor\u00f3s\u2010Gabarr\u00f3n","sequence":"additional","affiliation":[{"name":"INRAE, Universit\u00e9 C\u00f4te d'Azur, Institut Sophia Agrobiotech  06903 Sophia\u2010Antipolis France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Krishna","family":"Kumar","sequence":"additional","affiliation":[{"name":"Leibniz\u2010Institute of Vegetable and Ornamental Crops (IGZ) e.V.  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