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Although valuable for summarizing large gene lists into functional categories, it is often treated as the final interpretive step. In ecological omics, where functional annotations are frequently incomplete and experimental validation is often difficult, this reliance can lead to repetitive, generic conclusions that lack environmental and mechanistic specificity. Although previous literature has addressed the statistical and annotation\u2010related limitations of GO enrichment, its role in shaping the broader interpretive process has received less critical attention. Here, we highlight a conceptual weakness: the treatment of enriched GO terms as definitive biological insight. We focus particularly on ecological studies of non\u2010model organisms in complex, and heterogeneous environments. We discuss complementary strategies, including co\u2010expression network analysis, integration with environmental metadata, phylogenetically informed annotation, and AI\u2010assisted functional inference. To promote more context\u2010sensitive interpretation, we introduce the concept of\n                    <jats:italic>GO\u2010Deep<\/jats:italic>\n                    , which frames GO enrichment as a starting point for integrative, multilayered functional insight. By reframing GO enrichment as an entry point rather than a conclusion, ecological omics can move toward more mechanistically informative and environmentally grounded interpretations of high\u2010throughput data.\n                  <\/jats:p>","DOI":"10.1111\/mec.70570","type":"journal-article","created":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T07:26:12Z","timestamp":1791012372000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Problems With\n                    <scp>GO<\/scp>\n                    Enrichment as an Endpoint for Ecological Omics Interpretation"],"prefix":"10.1111","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6528-1187","authenticated-orcid":false,"given":"Ehsan Pashay","family":"Ahi","sequence":"first","affiliation":[{"name":"Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences University of Helsinki  Helsinki 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Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,10,3]]},"reference":[{"key":"e_1_2_14_2_1","doi-asserted-by":"publisher","DOI":"10.3389\/FPLS.2024.1377937\/BIBTEX"},{"key":"e_1_2_14_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598\u2010024\u201060261\u2010w"},{"key":"e_1_2_14_4_1","doi-asserted-by":"publisher","DOI":"10.1371\/JOURNAL.PCLM.0000403"},{"key":"e_1_2_14_5_1","doi-asserted-by":"publisher","DOI":"10.1002\/ece3.73007"},{"key":"e_1_2_14_6_1","doi-asserted-by":"publisher","DOI":"10.1002\/JEZ.B.70032"},{"key":"e_1_2_14_7_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12862\u2010025\u201002378\u20108"},{"key":"e_1_2_14_8_1","doi-asserted-by":"publisher","DOI":"10.1111\/MEC.17787"},{"key":"e_1_2_14_9_1","doi-asserted-by":"publisher","DOI":"10.1111\/MEC.17545"},{"key":"e_1_2_14_10_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4463"},{"key":"e_1_2_14_11_1","doi-asserted-by":"publisher","DOI":"10.1093\/GENETICS\/IYAD031"},{"key":"e_1_2_14_12_1","doi-asserted-by":"publisher","DOI":"10.1093\/NARGAB\/LQAE167"},{"key":"e_1_2_14_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/NAR\/GKAD1020"},{"key":"e_1_2_14_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010021\u201023579\u2010x"},{"key":"e_1_2_14_15_1","doi-asserted-by":"publisher","DOI":"10.1111\/1462\u20102920.16238"},{"key":"e_1_2_14_16_1","doi-asserted-by":"publisher","DOI":"10.1111\/NPH.19471"},{"key":"e_1_2_14_17_1","doi-asserted-by":"publisher","DOI":"10.1093\/NARGAB\/LQAA017"},{"key":"e_1_2_14_18_1","doi-asserted-by":"publisher","DOI":"10.1371\/JOURNAL.PCBI.1012346"},{"key":"e_1_2_14_19_1","doi-asserted-by":"publisher","DOI":"10.1093\/NAR\/GKW957"},{"key":"e_1_2_14_20_1","doi-asserted-by":"publisher","DOI":"10.1093\/BIOADV\/VBAF023"},{"key":"e_1_2_14_21_1","doi-asserted-by":"publisher","DOI":"10.1093\/BIOINFORMATICS\/BTAD549"},{"key":"e_1_2_14_22_1","doi-asserted-by":"publisher","DOI":"10.1093\/GIGASCIENCE\/GIAD088"},{"key":"e_1_2_14_23_1","doi-asserted-by":"publisher","DOI":"10.3389\/FPLS.2024.1309956\/BIBTEX"},{"key":"e_1_2_14_24_1","doi-asserted-by":"publisher","DOI":"10.1186\/S12859\u2010021\u201004370\u20107\/FIGURES\/8"},{"key":"e_1_2_14_25_1","doi-asserted-by":"publisher","DOI":"10.7554\/ELIFE.73425"},{"key":"e_1_2_14_26_1","doi-asserted-by":"publisher","DOI":"10.1186\/S13326\u2010016\u20100097\u20106\/FIGURES\/3"},{"key":"e_1_2_14_27_1","doi-asserted-by":"publisher","DOI":"10.1093\/BIB\/BBAE069"},{"key":"e_1_2_14_28_1","doi-asserted-by":"publisher","DOI":"10.1111\/MEC.14528"},{"key":"e_1_2_14_29_1","doi-asserted-by":"publisher","DOI":"10.1093\/MOLBEV\/MSAB293"},{"key":"e_1_2_14_30_1","doi-asserted-by":"publisher","DOI":"10.1007\/S00018\u2010023\u201004837\u20101"},{"key":"e_1_2_14_31_1","doi-asserted-by":"publisher","DOI":"10.1093\/NAR\/GKW1108"},{"key":"e_1_2_14_32_1","doi-asserted-by":"publisher","DOI":"10.1093\/NAR\/GKY1055"},{"key":"e_1_2_14_33_1","doi-asserted-by":"publisher","DOI":"10.1111\/NPH.18072"},{"key":"e_1_2_14_34_1","doi-asserted-by":"publisher","DOI":"10.1186\/S12864\u2010021\u201007659\u20102\/FIGURES\/7"},{"key":"e_1_2_14_35_1","doi-asserted-by":"publisher","DOI":"10.1186\/S40793\u2010022\u201000425\u20101\/FIGURES\/2"},{"key":"e_1_2_14_36_1","doi-asserted-by":"publisher","DOI":"10.1021\/ACS.EST.0C07262\/ASSET\/IMAGES\/LARGE\/ES0C07262_0005.JPEG"},{"key":"e_1_2_14_37_1","doi-asserted-by":"publisher","DOI":"10.1007\/978\u20101\u20100716\u20101103\u20106_8"},{"key":"e_1_2_14_38_1","doi-asserted-by":"publisher","DOI":"10.1016\/J.CEJ.2023.146507"},{"key":"e_1_2_14_39_1","doi-asserted-by":"publisher","DOI":"10.1093\/BIOINFORMATICS\/BTAC230"},{"key":"e_1_2_14_40_1","doi-asserted-by":"publisher","DOI":"10.1371\/JOURNAL.PCBI.1010348"},{"key":"e_1_2_14_41_1","doi-asserted-by":"publisher","DOI":"10.1073\/PNAS.1722151115\/SUPPL_FILE\/PNAS.1722151115.SAPP.PDF"},{"key":"e_1_2_14_42_1","doi-asserted-by":"publisher","DOI":"10.1073\/PNAS.1920779117\/SUPPL_FILE\/PNAS.1920779117.SAPP.PDF"},{"key":"e_1_2_14_43_1","doi-asserted-by":"publisher","DOI":"10.1128\/MSYSTEMS.00951\u201022\/SUPPL_FILE\/MSYSTEMS.00951\u201022\u2010S0009.DOCX"},{"key":"e_1_2_14_44_1","doi-asserted-by":"publisher","DOI":"10.1016\/J.CHEMOSPHERE.2023.138886"},{"key":"e_1_2_14_45_1","doi-asserted-by":"publisher","DOI":"10.3390\/E22040427"},{"key":"e_1_2_14_46_1","doi-asserted-by":"publisher","DOI":"10.1093\/DATABASE\/BAAC062"},{"key":"e_1_2_14_47_1","doi-asserted-by":"publisher","DOI":"10.1093\/G3JOURNAL\/JKAD072"},{"key":"e_1_2_14_48_1","doi-asserted-by":"publisher","DOI":"10.3389\/FMARS.2021.649909\/BIBTEX"},{"key":"e_1_2_14_49_1","doi-asserted-by":"publisher","DOI":"10.1109\/TCBBIO.2024.3498458"},{"key":"e_1_2_14_50_1","doi-asserted-by":"publisher","DOI":"10.1016\/J.CMPB.2015.12.002"},{"key":"e_1_2_14_51_1","doi-asserted-by":"publisher","DOI":"10.1111\/MEC.16588"},{"key":"e_1_2_14_52_1","doi-asserted-by":"publisher","DOI":"10.1007\/S10499\u2010026\u201002618\u20108"}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