{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:24Z","timestamp":1772138064725,"version":"3.50.1"},"reference-count":69,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2023,8,4]],"date-time":"2023-08-04T00:00:00Z","timestamp":1691107200000},"content-version":"vor","delay-in-days":3,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Fondation Sant\u00e9 and the Onassis Foundation"},{"DOI":"10.13039\/501100013209","name":"Hellenic Foundation for Research and Innovation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100013209","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>\u2003<\/jats:title>\n                    <jats:p>Summary: Functional enrichment is the process of identifying implicated functional terms from a given input list of genes or proteins. In this article, we present Flame (v2.0), a web tool which offers a combinatorial approach through merging and visualizing results from widely used functional enrichment applications while also allowing various flexible input options. In this version, Flame utilizes the aGOtool, g: Profiler, WebGestalt, and Enrichr pipelines and presents their outputs separately or in combination following a visual analytics approach. For intuitive representations and easier interpretation, it uses interactive plots such as parameterizable networks, heatmaps, barcharts, and scatter plots. Users can also: (i) handle multiple protein\/gene lists and analyse union and intersection sets simultaneously through interactive UpSet plots, (ii) automatically extract genes and proteins from free text through text-mining and Named Entity Recognition (NER) techniques, (iii) upload single nucleotide polymorphisms (SNPs) and extract their relative genes, or (iv) analyse multiple lists of differentially expressed proteins\/genes after selecting them interactively from a parameterizable volcano plot. Compared to the previous version of 197 supported organisms, Flame (v2.0) currently allows enrichment for 14\u00a0436 organisms.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Web Application: http:\/\/flame.pavlopouloslab.info. Code: https:\/\/github.com\/PavlopoulosLab\/Flame. Docker: https:\/\/hub.docker.com\/r\/pavlopouloslab\/flame.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad490","type":"journal-article","created":{"date-parts":[[2023,8,4]],"date-time":"2023-08-04T12:05:43Z","timestamp":1691150743000},"source":"Crossref","is-referenced-by-count":16,"title":["Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9132-8981","authenticated-orcid":false,"given":"Evangelos","family":"Karatzas","sequence":"first","affiliation":[{"name":"Institute for Fundamental Biomedical Research, BSRC \u201cAlexander Fleming\u201d , Vari (Athens), 16672, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2870-2931","authenticated-orcid":false,"given":"Fotis A","family":"Baltoumas","sequence":"additional","affiliation":[{"name":"Institute for Fundamental Biomedical Research, BSRC \u201cAlexander Fleming\u201d , Vari (Athens), 16672, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eleni","family":"Aplakidou","sequence":"additional","affiliation":[{"name":"Institute for Fundamental Biomedical Research, BSRC \u201cAlexander Fleming\u201d , Vari (Athens), 16672, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Panagiota I","family":"Kontou","sequence":"additional","affiliation":[{"name":"Department of Mathematics, University of Thessaly , Lamia, 35100, Greece"},{"name":"Department of Computer Science and Biomedical Informatics, University of Thessaly , Lamia, 35131, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Panos","family":"Stathopoulos","sequence":"additional","affiliation":[{"name":"1st Department of Neurology, Eginition Hospital , Athens, 11528, Greece"},{"name":"School of Medicine, National and Kapodistrian University of Athens , Athens, 11527, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leonidas","family":"Stefanis","sequence":"additional","affiliation":[{"name":"1st Department of Neurology, Eginition Hospital , Athens, 11528, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4935-2325","authenticated-orcid":false,"given":"Pantelis G","family":"Bagos","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Biomedical Informatics, University of Thessaly , Lamia, 35131, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4577-8276","authenticated-orcid":false,"given":"Georgios A","family":"Pavlopoulos","sequence":"additional","affiliation":[{"name":"Institute for Fundamental Biomedical Research, BSRC \u201cAlexander Fleming\u201d , Vari (Athens), 16672, Greece"},{"name":"Center of Basic Research, Biomedical Research Foundation of the Academy of Athens , Athens, 11527, 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