{"id":"https://openalex.org/W4391654308","doi":"https://doi.org/10.1186/s12859-024-05676-y","title":"vissE: a versatile tool to identify and visualise higher-order molecular phenotypes from functional enrichment analysis","display_name":"vissE: a versatile tool to identify and visualise higher-order molecular phenotypes from functional enrichment analysis","publication_year":2024,"publication_date":"2024-02-08","ids":{"openalex":"https://openalex.org/W4391654308","doi":"https://doi.org/10.1186/s12859-024-05676-y","pmid":"https://pubmed.ncbi.nlm.nih.gov/38331751"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-024-05676-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05676-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05676-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05676-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007306514","display_name":"Dharmesh D. Bhuva","orcid":"https://orcid.org/0000-0002-6398-9157"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]},{"id":"https://openalex.org/I4210137740","display_name":"South Australian Health and Medical Research Institute","ror":"https://ror.org/03e3kts03","country_code":"AU","type":"healthcare","lineage":["https://openalex.org/I4210137740"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Dharmesh D. Bhuva","raw_affiliation_strings":["Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia. dharmesh.bhuva@adelaide.edu.au","Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia. dharmesh.bhuva@adelaide.edu.au","South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia. dharmesh.bhuva@adelaide.edu.au","Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia. dharmesh.bhuva@adelaide.edu.au","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia. dharmesh.bhuva@adelaide.edu.au","institution_ids":["https://openalex.org/I196021976"]},{"raw_affiliation_string":"South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia. dharmesh.bhuva@adelaide.edu.au","institution_ids":["https://openalex.org/I4210137740"]},{"raw_affiliation_string":"Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia","institution_ids":["https://openalex.org/I196021976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088957393","display_name":"Chin Wee Tan","orcid":"https://orcid.org/0000-0001-9695-7218"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]},{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Chin Wee Tan","raw_affiliation_strings":["Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia","Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia","Fraser Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, 4102, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia","institution_ids":["https://openalex.org/I196021976"]},{"raw_affiliation_string":"Fraser Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, 4102, Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100432410","display_name":"Ning Liu","orcid":"https://orcid.org/0000-0002-9487-9305"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]},{"id":"https://openalex.org/I5681781","display_name":"The University of Adelaide","ror":"https://ror.org/00892tw58","country_code":"AU","type":"education","lineage":["https://openalex.org/I5681781"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Ning Liu","raw_affiliation_strings":["Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia","Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia","South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia","institution_ids":["https://openalex.org/I196021976"]},{"raw_affiliation_string":"South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia","institution_ids":["https://openalex.org/I5681781"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028078153","display_name":"Holly J. Whitfield","orcid":"https://orcid.org/0000-0002-7282-387X"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]},{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["AU","GB"],"is_corresponding":false,"raw_author_name":"Holly J. Whitfield","raw_affiliation_strings":["Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia","Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia","Wellcome Sanger Institute, Hinxton, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia","institution_ids":["https://openalex.org/I196021976"]},{"raw_affiliation_string":"Wellcome Sanger Institute, Hinxton, UK","institution_ids":["https://openalex.org/I2802476451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063863213","display_name":"Nicholas Papachristos","orcid":null},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Nicholas Papachristos","raw_affiliation_strings":["Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia","Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia","institution_ids":["https://openalex.org/I196021976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087978393","display_name":"Sam Lee","orcid":"https://orcid.org/0000-0002-6805-4051"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Samuel C. Lee","raw_affiliation_strings":["Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia","Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia","institution_ids":["https://openalex.org/I196021976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032063587","display_name":"Malvika Kharbanda","orcid":"https://orcid.org/0000-0001-9726-3023"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]},{"id":"https://openalex.org/I5681781","display_name":"The University of Adelaide","ror":"https://ror.org/00892tw58","country_code":"AU","type":"education","lineage":["https://openalex.org/I5681781"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Malvika Kharbanda","raw_affiliation_strings":["Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia","Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia","South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia","institution_ids":["https://openalex.org/I196021976"]},{"raw_affiliation_string":"South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia","institution_ids":["https://openalex.org/I5681781"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038054571","display_name":"Ahmed Mohamed","orcid":"https://orcid.org/0000-0001-6507-5300"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Ahmed Mohamed","raw_affiliation_strings":["Colonial Foundation Healthy Ageing Centre, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia","Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia","Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Colonial Foundation Healthy Ageing Centre, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia","institution_ids":["https://openalex.org/I196021976"]},{"raw_affiliation_string":"Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia","institution_ids":["https://openalex.org/I196021976"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018252802","display_name":"Melissa J. Davis","orcid":"https://orcid.org/0000-0003-4864-7033"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]},{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]},{"id":"https://openalex.org/I5681781","display_name":"The University of Adelaide","ror":"https://ror.org/00892tw58","country_code":"AU","type":"education","lineage":["https://openalex.org/I5681781"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Melissa J. Davis","raw_affiliation_strings":["Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia","Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia","Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia","Fraser Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, 4102, Australia","South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia","institution_ids":["https://openalex.org/I196021976"]},{"raw_affiliation_string":"Fraser Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, 4102, Australia","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia","institution_ids":["https://openalex.org/I5681781"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5007306514"],"corresponding_institution_ids":["https://openalex.org/I165779595","https://openalex.org/I196021976","https://openalex.org/I4210137740"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.8089,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.90770994,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"25","issue":"1","first_page":"64","last_page":"64"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9977999925613403,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9976999759674072,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7081806659698486},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6551901698112488},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6296483278274536},{"id":"https://openalex.org/keywords/adaptability","display_name":"Adaptability","score":0.5697799324989319},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4801044762134552},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4624612033367157},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4597734212875366},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3508042097091675},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.27331653237342834},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.13089659810066223}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7081806659698486},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6551901698112488},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6296483278274536},{"id":"https://openalex.org/C177606310","wikidata":"https://www.wikidata.org/wiki/Q5674297","display_name":"Adaptability","level":2,"score":0.5697799324989319},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4801044762134552},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4624612033367157},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4597734212875366},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3508042097091675},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27331653237342834},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.13089659810066223},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-024-05676-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05676-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05676-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38331751","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38331751","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10854147","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10854147","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10854147/pdf/12859_2024_Article_5676.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:b8ade091f46b447d94b4602e9efe1672","is_oa":true,"landing_page_url":"https://doaj.org/article/b8ade091f46b447d94b4602e9efe1672","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 25, Iss 1, Pp 1-22 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-024-05676-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05676-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05676-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320313923","display_name":"Australian Lions Childhood Cancer Research Foundation","ror":null},{"id":"https://openalex.org/F4320320438","display_name":"National Breast Cancer Foundation","ror":"https://ror.org/0120ky124"},{"id":"https://openalex.org/F4320322858","display_name":"State Government of Victoria","ror":"https://ror.org/02xvc5r05"},{"id":"https://openalex.org/F4320324006","display_name":"Cure Brain Cancer Foundation","ror":"https://ror.org/02db9yt31"},{"id":"https://openalex.org/F4320330800","display_name":"Colonial Foundation","ror":null},{"id":"https://openalex.org/F4320334707","display_name":"Cancer Council Victoria","ror":"https://ror.org/023m51b03"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4391654308.pdf"},"referenced_works_count":74,"referenced_works":["https://openalex.org/W1562973462","https://openalex.org/W1969353942","https://openalex.org/W1989277387","https://openalex.org/W1995683190","https://openalex.org/W2010327215","https://openalex.org/W2013515157","https://openalex.org/W2024315189","https://openalex.org/W2025855398","https://openalex.org/W2035618305","https://openalex.org/W2045005503","https://openalex.org/W2045729458","https://openalex.org/W2056044063","https://openalex.org/W2084168100","https://openalex.org/W2097948046","https://openalex.org/W2100980426","https://openalex.org/W2103017472","https://openalex.org/W2107018762","https://openalex.org/W2110905563","https://openalex.org/W2114104545","https://openalex.org/W2120024428","https://openalex.org/W2121280864","https://openalex.org/W2130410032","https://openalex.org/W2133465414","https://openalex.org/W2134477837","https://openalex.org/W2138207763","https://openalex.org/W2138255346","https://openalex.org/W2143947098","https://openalex.org/W2144907278","https://openalex.org/W2161793142","https://openalex.org/W2169589032","https://openalex.org/W2171030481","https://openalex.org/W2171437346","https://openalex.org/W2214074259","https://openalex.org/W2466314544","https://openalex.org/W2497752945","https://openalex.org/W2516455020","https://openalex.org/W2540833380","https://openalex.org/W2606062902","https://openalex.org/W2756978353","https://openalex.org/W2774736917","https://openalex.org/W2783018806","https://openalex.org/W2868772566","https://openalex.org/W2888939561","https://openalex.org/W2900032527","https://openalex.org/W2901068426","https://openalex.org/W2907514116","https://openalex.org/W2910111050","https://openalex.org/W2912405236","https://openalex.org/W2928665623","https://openalex.org/W2947925171","https://openalex.org/W2949177718","https://openalex.org/W2954544233","https://openalex.org/W2967538289","https://openalex.org/W2994535290","https://openalex.org/W3003058300","https://openalex.org/W3015459088","https://openalex.org/W3041230641","https://openalex.org/W3090990034","https://openalex.org/W3092495933","https://openalex.org/W3095104045","https://openalex.org/W3104267360","https://openalex.org/W3129476455","https://openalex.org/W3134165232","https://openalex.org/W3158950527","https://openalex.org/W3158998710","https://openalex.org/W3164271582","https://openalex.org/W3175752499","https://openalex.org/W3198511950","https://openalex.org/W4233698560","https://openalex.org/W4238308465","https://openalex.org/W4241872665","https://openalex.org/W4248625327","https://openalex.org/W4281620292","https://openalex.org/W4375954697"],"related_works":["https://openalex.org/W2357124094","https://openalex.org/W2387399993","https://openalex.org/W2389739210","https://openalex.org/W2348924972","https://openalex.org/W2365736347","https://openalex.org/W2047454415","https://openalex.org/W2070040999","https://openalex.org/W2387293848","https://openalex.org/W2250140200","https://openalex.org/W3121791438"],"abstract_inverted_index":{"Functional":[0],"analysis":[1,8,58,112,140],"of":[2,19,29,87,113],"high":[3],"throughput":[4],"experiments":[5],"using":[6],"pathway":[7,139],"is":[9],"now":[10],"ubiquitous.":[11],"Though":[12],"powerful,":[13],"these":[14],"methods":[15],"often":[16],"produce":[17],"thousands":[18],"redundant":[20],"results":[21,30],"owing":[22],"to":[23,39,43,73,78,98,109,132],"knowledgebase":[24],"redundancies":[25],"upstream.":[26],"This":[27],"scale":[28],"hinders":[31],"extensive":[32],"exploration":[33],"by":[34,95],"biologists":[35,143],"and":[36,46,59,68,104,138],"can":[37],"lead":[38],"investigator":[40],"biases":[41],"due":[42],"previous":[44],"knowledge":[45],"expectations.":[47],"To":[48],"address":[49],"this":[50],"issue,":[51],"we":[52,120],"present":[53],"vissE,":[54],"a":[55,84,110,114],"flexible":[56],"network-based":[57],"visualisation":[60,71],"tool":[61],"that":[62,124],"organises":[63],"information":[64],"into":[65],"semantic":[66],"categories":[67],"provides":[69],"various":[70],"modules":[72],"characterise":[74],"them":[75],"with":[76],"respect":[77],"the":[79,88],"underlying":[80],"data,":[81,119],"thus":[82],"providing":[83],"comprehensive":[85],"view":[86],"biological":[89],"system.":[90],"We":[91],"demonstrate":[92],"vissE's":[93],"versatility":[94],"applying":[96],"it":[97],"three":[99],"different":[100],"technologies:":[101],"bulk,":[102],"single-cell":[103],"spatial":[105,117],"transcriptomics.":[106],"Applying":[107],"vissE":[108,131],"factor":[111],"breast":[115],"cancer":[116],"transcriptomic":[118],"identified":[121],"stromal":[122],"phenotypes":[123],"support":[125],"tumour":[126],"dissemination.":[127],"Its":[128],"adaptability":[129],"allows":[130],"enhance":[133],"all":[134],"existing":[135],"gene-set":[136],"enrichment":[137],"workflows,":[141],"empowering":[142],"during":[144],"molecular":[145],"discovery.":[146]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-07-10T07:45:09.275182","created_date":"2025-10-10T00:00:00"}
