{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T15:25:10Z","timestamp":1753889110318,"version":"3.37.3"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2023,5,9]],"date-time":"2023-05-09T00:00:00Z","timestamp":1683590400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100020840","name":"Australian Research Data Commons","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100020840","id-type":"DOI","asserted-by":"publisher"}]},{"name":"olonial Foundation Healthy Ageing Centre"},{"DOI":"10.13039\/501100000951","name":"Cancer Council Victoria","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000951","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Australian Lions Childhood Cancer Foundation"},{"name":"Betty Smyth Centenary Fellowship in Bioinformatics"},{"name":"Cure Brain Cancer Foundation and National Breast Cancer Foundation","award":["CBCNBCF-19-009"],"award-info":[{"award-number":["CBCNBCF-19-009"]}]},{"DOI":"10.13039\/501100004752","name":"Victorian Government","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004752","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Discretionary Lab budget"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Gene-set analysis (GSA) dominates the functional interpretation of omics data and downstream hypothesis generation. Despite its ability to summarise thousands of measurements into semantically interpretable components, GSA often results in hundreds of significantly enriched gene-sets. However, summarisation and effective visualisation of GSA results to facilitate hypothesis generation is still lacking. While some webservers provide gene-set visualization tools, there is still a need for tools that can effectively summarize and guide exploration of GSA results. To enable versatility, webservers accept gene lists as input, however, none provide end-to-end solutions for emerging data types such as single-cell and spatial omics. Here, we present vissE.Cloud, a webserver for end-to-end gene-set analysis, offering gene-set summarisation and highly interactive visualisation. vissE.Cloud uses algorithms from our earlier R package vissE to summarise GSA results by identifying biological themes. We maintain versatility by allowing analysis of gene lists, as well as, analysis of raw single-cell and spatial omics data, including CosMx and Xenium data, making vissE.Cloud the first webserver to provide end-to-end gene-set analysis of sub-cellular localised spatial data. Structuring the results hierarchically allows swift interactive investigations of results at the gene, gene-set, and clusters level. vissE.Cloud is freely available at https:\/\/www.vissE.Cloud.<\/jats:p>","DOI":"10.1093\/nar\/gkad337","type":"journal-article","created":{"date-parts":[[2023,5,10]],"date-time":"2023-05-10T19:31:53Z","timestamp":1683747113000},"page":"W593-W600","source":"Crossref","is-referenced-by-count":4,"title":["vissE.cloud: a webserver to visualise higher order molecular phenotypes from enrichment analysis"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6507-5300","authenticated-orcid":false,"given":"Ahmed","family":"Mohamed","sequence":"first","affiliation":[{"name":"Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research , Melbourne , VIC 3052, Australia"},{"name":"Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne , Parkville , VIC 3010, Australia"},{"name":"Colonial Foundation Healthy Ageing Centre, Walter and Eliza Hall Institute of Medical Research , Melbourne , VIC 3052, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6398-9157","authenticated-orcid":false,"given":"Dharmesh D","family":"Bhuva","sequence":"additional","affiliation":[{"name":"Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research , Melbourne , VIC 3052, Australia"},{"name":"Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne , Parkville , VIC 3010, Australia"},{"name":"South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide , Adelaide , SA 5005, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sam","family":"Lee","sequence":"additional","affiliation":[{"name":"Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research , Melbourne , VIC 3052, Australia"},{"name":"Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne , Parkville , VIC 3010, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ning","family":"Liu","sequence":"additional","affiliation":[{"name":"Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research , Melbourne , VIC 3052, Australia"},{"name":"Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne , Parkville , VIC 3010, Australia"},{"name":"South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide , Adelaide , SA 5005, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chin\u00a0Wee","family":"Tan","sequence":"additional","affiliation":[{"name":"Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research , Melbourne , VIC 3052, Australia"},{"name":"Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne , Parkville , VIC 3010, Australia"},{"name":"Frazer Institute, Faculty of Medicine, The University of Queensland , Brisbane ,\u00a0 QLD 4102, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4864-7033","authenticated-orcid":false,"given":"Melissa J","family":"Davis","sequence":"additional","affiliation":[{"name":"Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research , Melbourne , VIC 3052, Australia"},{"name":"Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne , Parkville , VIC 3010, Australia"},{"name":"South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide , Adelaide , SA 5005, Australia"},{"name":"Frazer Institute, Faculty of Medicine, The University of Queensland , Brisbane ,\u00a0 QLD 4102, Australia"},{"name":"Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne , Parkville , VIC 3010, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,5,9]]},"reference":[{"key":"2023070504573954700_B1","first-page":"1438","article-title":"From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline","volume":"5","author":"Chen","year":"2016","journal-title":"F1000Res"},{"key":"2023070504573954700_B2","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1186\/1471-2105-9-559","article-title":"WGCNA: an R package for weighted correlation network analysis","volume":"9","author":"Langfelder","year":"2008","journal-title":"BMC 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