{"id":"https://openalex.org/W2046333076","doi":"https://doi.org/10.1186/s12859-015-0578-0","title":"VISIONET: intuitive visualisation of overlapping transcription factor networks, with applications in cardiogenic gene discovery","display_name":"VISIONET: intuitive visualisation of overlapping transcription factor networks, with applications in cardiogenic gene discovery","publication_year":2015,"publication_date":"2015-04-30","ids":{"openalex":"https://openalex.org/W2046333076","doi":"https://doi.org/10.1186/s12859-015-0578-0","mag":"2046333076","pmid":"https://pubmed.ncbi.nlm.nih.gov/25929466"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-015-0578-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0578-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0578-0","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/s12859-015-0578-0","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016142657","display_name":"Hieu T. Nim","orcid":"https://orcid.org/0000-0001-9320-0236"},"institutions":[{"id":"https://openalex.org/I2801239119","display_name":"Australian Regenerative Medicine Institute","ror":"https://ror.org/02qa5kg76","country_code":"AU","type":"facility","lineage":["https://openalex.org/I2801037857","https://openalex.org/I2801239119","https://openalex.org/I56590836"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Hieu T Nim","raw_affiliation_strings":["Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia. hieu.nim@monash.edu","Systems Biology Institute (SBI) Australia, Monash University, Clayton, VIC, 3800, Australia. hieu.nim@monash.edu","Australian Regenerative Medicine Institute, Monash University, Clayton, Australia","Systems Biology Institute (SBI) Australia, Monash University, Clayton, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia. hieu.nim@monash.edu","institution_ids":["https://openalex.org/I2801239119"]},{"raw_affiliation_string":"Systems Biology Institute (SBI) Australia, Monash University, Clayton, VIC, 3800, Australia. hieu.nim@monash.edu","institution_ids":["https://openalex.org/I56590836"]},{"raw_affiliation_string":"Australian Regenerative Medicine Institute, Monash University, Clayton, Australia","institution_ids":["https://openalex.org/I2801239119","https://openalex.org/I56590836"]},{"raw_affiliation_string":"Systems Biology Institute (SBI) Australia, Monash University, Clayton, Australia","institution_ids":["https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084836557","display_name":"Milena B. Furtado","orcid":"https://orcid.org/0000-0003-1387-325X"},"institutions":[{"id":"https://openalex.org/I2801239119","display_name":"Australian Regenerative Medicine Institute","ror":"https://ror.org/02qa5kg76","country_code":"AU","type":"facility","lineage":["https://openalex.org/I2801037857","https://openalex.org/I2801239119","https://openalex.org/I56590836"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Milena B Furtado","raw_affiliation_strings":["Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia. milena.furtado@monash.edu","Australian Regenerative Medicine Institute, Monash University, Clayton, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia. milena.furtado@monash.edu","institution_ids":["https://openalex.org/I2801239119"]},{"raw_affiliation_string":"Australian Regenerative Medicine Institute, Monash University, Clayton, Australia","institution_ids":["https://openalex.org/I2801239119","https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049693824","display_name":"Mauro W. Costa","orcid":"https://orcid.org/0000-0003-3579-8625"},"institutions":[{"id":"https://openalex.org/I2801239119","display_name":"Australian Regenerative Medicine Institute","ror":"https://ror.org/02qa5kg76","country_code":"AU","type":"facility","lineage":["https://openalex.org/I2801037857","https://openalex.org/I2801239119","https://openalex.org/I56590836"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Mauro W Costa","raw_affiliation_strings":["Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia. mauro.dacosta@monash.edu","Australian Regenerative Medicine Institute, Monash University, Clayton, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia. mauro.dacosta@monash.edu","institution_ids":["https://openalex.org/I2801239119"]},{"raw_affiliation_string":"Australian Regenerative Medicine Institute, Monash University, Clayton, Australia","institution_ids":["https://openalex.org/I2801239119","https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042049867","display_name":"Nadia Rosenthal","orcid":"https://orcid.org/0000-0002-7599-7365"},"institutions":[{"id":"https://openalex.org/I2801239119","display_name":"Australian Regenerative Medicine Institute","ror":"https://ror.org/02qa5kg76","country_code":"AU","type":"facility","lineage":["https://openalex.org/I2801037857","https://openalex.org/I2801239119","https://openalex.org/I56590836"]},{"id":"https://openalex.org/I4210101049","display_name":"Lung Institute","ror":"https://ror.org/016978714","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210101049"]},{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU","GB","US"],"is_corresponding":false,"raw_author_name":"Nadia A Rosenthal","raw_affiliation_strings":["Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia. nadia.rosenthal@monash.edu","National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK. nadia.rosenthal@monash.edu","Systems Biology Institute (SBI) Australia, Monash University, Clayton, VIC, 3800, Australia. nadia.rosenthal@monash.edu","National Heart and Lung Institute, Imperial College London, London, UK","Australian Regenerative Medicine Institute, Monash University, Clayton, Australia","Systems Biology Institute (SBI) Australia, Monash University, Clayton, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia. nadia.rosenthal@monash.edu","institution_ids":["https://openalex.org/I2801239119"]},{"raw_affiliation_string":"National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK. nadia.rosenthal@monash.edu","institution_ids":["https://openalex.org/I4210101049"]},{"raw_affiliation_string":"Systems Biology Institute (SBI) Australia, Monash University, Clayton, VIC, 3800, Australia. nadia.rosenthal@monash.edu","institution_ids":["https://openalex.org/I56590836"]},{"raw_affiliation_string":"National Heart and Lung Institute, Imperial College London, London, UK","institution_ids":["https://openalex.org/I47508984"]},{"raw_affiliation_string":"Australian Regenerative Medicine Institute, Monash University, Clayton, Australia","institution_ids":["https://openalex.org/I2801239119","https://openalex.org/I56590836"]},{"raw_affiliation_string":"Systems Biology Institute (SBI) Australia, Monash University, Clayton, Australia","institution_ids":["https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086835862","display_name":"Hiroaki Kitano","orcid":"https://orcid.org/0000-0002-3589-1953"},"institutions":[{"id":"https://openalex.org/I142637625","display_name":"Okinawa Institute of Science and Technology Graduate University","ror":"https://ror.org/02qg15b79","country_code":"JP","type":"education","lineage":["https://openalex.org/I142637625"]},{"id":"https://openalex.org/I2801239119","display_name":"Australian Regenerative Medicine Institute","ror":"https://ror.org/02qa5kg76","country_code":"AU","type":"facility","lineage":["https://openalex.org/I2801037857","https://openalex.org/I2801239119","https://openalex.org/I56590836"]},{"id":"https://openalex.org/I4210118579","display_name":"Systems Biology Institute","ror":"https://ror.org/02c7akf81","country_code":"JP","type":"nonprofit","lineage":["https://openalex.org/I4210118579"]},{"id":"https://openalex.org/I4210122684","display_name":"Sony Computer Science Laboratories","ror":"https://ror.org/02nc46417","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210122684"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU","JP"],"is_corresponding":false,"raw_author_name":"Hiroaki Kitano","raw_affiliation_strings":["Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia. kitano@sbi.jp","Okinawa Institute of Science and Technology, Onna, Onna-son, Kunigami, Okinawa, Japan. kitano@sbi.jp","Sony Computer Science Laboratories, Inc., Higashigotanda, Shinagawa, Tokyo, Japan. kitano@sbi.jp","Systems Biology Institute (SBI) Australia, Monash University, Clayton, VIC, 3800, Australia. kitano@sbi.jp","Sony Computer Science Laboratories, Inc., Shinagawa, Japan","Australian Regenerative Medicine Institute, Monash University, Clayton, Australia","Systems Biology Institute (SBI) Australia, Monash University, Clayton, Australia","Okinawa Institute of Science and Technology, Kunigami, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia. kitano@sbi.jp","institution_ids":["https://openalex.org/I2801239119"]},{"raw_affiliation_string":"Okinawa Institute of Science and Technology, Onna, Onna-son, Kunigami, Okinawa, Japan. kitano@sbi.jp","institution_ids":["https://openalex.org/I142637625"]},{"raw_affiliation_string":"Sony Computer Science Laboratories, Inc., Higashigotanda, Shinagawa, Tokyo, Japan. kitano@sbi.jp","institution_ids":["https://openalex.org/I4210122684"]},{"raw_affiliation_string":"Systems Biology Institute (SBI) Australia, Monash University, Clayton, VIC, 3800, Australia. kitano@sbi.jp","institution_ids":["https://openalex.org/I4210118579"]},{"raw_affiliation_string":"Sony Computer Science Laboratories, Inc., Shinagawa, Japan","institution_ids":["https://openalex.org/I4210122684"]},{"raw_affiliation_string":"Australian Regenerative Medicine Institute, Monash University, Clayton, Australia","institution_ids":["https://openalex.org/I2801239119","https://openalex.org/I56590836"]},{"raw_affiliation_string":"Systems Biology Institute (SBI) Australia, Monash University, Clayton, Australia","institution_ids":["https://openalex.org/I56590836"]},{"raw_affiliation_string":"Okinawa Institute of Science and Technology, Kunigami, Japan","institution_ids":["https://openalex.org/I142637625"]}]},{"author_position":"last","author":{"id":null,"display_name":"Sarah E Boyd","orcid":null},"institutions":[{"id":"https://openalex.org/I2801239119","display_name":"Australian Regenerative Medicine Institute","ror":"https://ror.org/02qa5kg76","country_code":"AU","type":"facility","lineage":["https://openalex.org/I2801037857","https://openalex.org/I2801239119","https://openalex.org/I56590836"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Sarah E Boyd","raw_affiliation_strings":["Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia. sarah.boyd@monash.edu","Systems Biology Institute (SBI) Australia, Monash University, Clayton, VIC, 3800, Australia. sarah.boyd@monash.edu","Systems Biology Institute (SBI) Australia, Monash University, Clayton, Australia","Australian Regenerative Medicine Institute, Monash University, Clayton, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia. sarah.boyd@monash.edu","institution_ids":["https://openalex.org/I2801239119"]},{"raw_affiliation_string":"Systems Biology Institute (SBI) Australia, Monash University, Clayton, VIC, 3800, Australia. sarah.boyd@monash.edu","institution_ids":["https://openalex.org/I56590836"]},{"raw_affiliation_string":"Systems Biology Institute (SBI) Australia, Monash University, Clayton, Australia","institution_ids":["https://openalex.org/I56590836"]},{"raw_affiliation_string":"Australian Regenerative Medicine Institute, Monash University, Clayton, Australia","institution_ids":["https://openalex.org/I2801239119","https://openalex.org/I56590836"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5016142657"],"corresponding_institution_ids":["https://openalex.org/I2801239119","https://openalex.org/I56590836"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.4518,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.65771631,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"16","issue":"1","first_page":"141","last_page":"141"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.994700014591217,"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":0.994700014591217,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9883999824523926,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9853000044822693,"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/transcription-factor","display_name":"Transcription factor","score":0.62360680103302},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6199865937232971},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5964111089706421},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5744409561157227},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5025789737701416},{"id":"https://openalex.org/keywords/gata4","display_name":"GATA4","score":0.4923912286758423},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.41547727584838867},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3716794550418854},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.35496920347213745},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3301602602005005},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3139232099056244},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.23442873358726501},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22171679139137268}],"concepts":[{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.62360680103302},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6199865937232971},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5964111089706421},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5744409561157227},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5025789737701416},{"id":"https://openalex.org/C116186050","wikidata":"https://www.wikidata.org/wiki/Q4039110","display_name":"GATA4","level":4,"score":0.4923912286758423},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.41547727584838867},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3716794550418854},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.35496920347213745},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3301602602005005},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3139232099056244},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.23442873358726501},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22171679139137268}],"mesh":[{"descriptor_ui":"D000328","descriptor_name":"Adult","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000328","descriptor_name":"Adult","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000328","descriptor_name":"Adult","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002478","descriptor_name":"Cells, Cultured","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002478","descriptor_name":"Cells, Cultured","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002478","descriptor_name":"Cells, Cultured","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005347","descriptor_name":"Fibroblasts","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D005347","descriptor_name":"Fibroblasts","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D005347","descriptor_name":"Fibroblasts","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D005347","descriptor_name":"Fibroblasts","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005347","descriptor_name":"Fibroblasts","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005347","descriptor_name":"Fibroblasts","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006321","descriptor_name":"Heart","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D006321","descriptor_name":"Heart","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D006321","descriptor_name":"Heart","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018507","descriptor_name":"Gene Expression Regulation, Developmental","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018507","descriptor_name":"Gene Expression Regulation, Developmental","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018507","descriptor_name":"Gene Expression Regulation, Developmental","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020825","descriptor_name":"T-Box Domain Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020825","descriptor_name":"T-Box Domain Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020825","descriptor_name":"T-Box Domain Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D050991","descriptor_name":"GATA4 Transcription Factor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D050991","descriptor_name":"GATA4 Transcription Factor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D050991","descriptor_name":"GATA4 Transcription Factor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056726","descriptor_name":"Genetic Association Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056726","descriptor_name":"Genetic Association Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056726","descriptor_name":"Genetic Association Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-015-0578-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0578-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0578-0","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:25929466","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25929466","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:europepmc.org:3387751","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4426166","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:mouseion.jax.org:stfb2015-1109","is_oa":false,"landing_page_url":"https://mouseion.jax.org/stfb2015/110","pdf_url":null,"source":{"id":"https://openalex.org/S4377196421","display_name":"The Mouseion at the JAXlibrary (Jackson Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210115256","host_organization_name":"Jackson Laboratory","host_organization_lineage":["https://openalex.org/I4210115256"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Research 2015","raw_type":"text"},{"id":"pmh:oai:spiral.imperial.ac.uk:10044/1/40704","is_oa":true,"landing_page_url":"http://hdl.handle.net/10044/1/40704","pdf_url":null,"source":{"id":"https://openalex.org/S4306401396","display_name":"Spiral (Imperial College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I47508984","host_organization_name":"Imperial College London","host_organization_lineage":["https://openalex.org/I47508984"],"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":"","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1186/s12859-015-0578-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0578-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0578-0","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/F4320315885","display_name":"Australian Government","ror":"https://ror.org/0314h5y94"},{"id":"https://openalex.org/F4320322858","display_name":"State Government of Victoria","ror":"https://ror.org/02xvc5r05"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2046333076.pdf","grobid_xml":"https://content.openalex.org/works/W2046333076.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1528597731","https://openalex.org/W1967656072","https://openalex.org/W1976209715","https://openalex.org/W1981748685","https://openalex.org/W1981904270","https://openalex.org/W1984380128","https://openalex.org/W1988878467","https://openalex.org/W1996361830","https://openalex.org/W1996588166","https://openalex.org/W2007631412","https://openalex.org/W2010502047","https://openalex.org/W2023098599","https://openalex.org/W2036145288","https://openalex.org/W2038264484","https://openalex.org/W2039379704","https://openalex.org/W2040213004","https://openalex.org/W2045998016","https://openalex.org/W2060181055","https://openalex.org/W2071353749","https://openalex.org/W2086798689","https://openalex.org/W2097836010","https://openalex.org/W2103237492","https://openalex.org/W2103945987","https://openalex.org/W2104197938","https://openalex.org/W2108980486","https://openalex.org/W2117364474","https://openalex.org/W2129660202","https://openalex.org/W2136494222","https://openalex.org/W2140406586","https://openalex.org/W2146053439","https://openalex.org/W2146111380","https://openalex.org/W2153921000","https://openalex.org/W2154201149","https://openalex.org/W2154847292","https://openalex.org/W2155142785","https://openalex.org/W2158453355","https://openalex.org/W2159675211","https://openalex.org/W2159679884","https://openalex.org/W2166283098","https://openalex.org/W2167202160","https://openalex.org/W2167482691","https://openalex.org/W2169333371","https://openalex.org/W2169696276","https://openalex.org/W2407192161"],"related_works":["https://openalex.org/W2774895225","https://openalex.org/W2068608913","https://openalex.org/W2059070580","https://openalex.org/W2001356598","https://openalex.org/W2054338068","https://openalex.org/W2983482405","https://openalex.org/W2050558000","https://openalex.org/W2090429499","https://openalex.org/W1878240916","https://openalex.org/W2461435563"],"abstract_inverted_index":{"BACKGROUND:":[0],"Existing":[1],"de":[2],"novo":[3],"software":[4],"platforms":[5],"have":[6,173],"largely":[7],"overlooked":[8],"a":[9,47,79,136],"valuable":[10],"resource,":[11],"the":[12,15,112,119,156],"expertise":[13],"of":[14,123,158],"intended":[16],"biologist":[17],"users.":[18],"Typical":[19],"data":[20,103],"representations":[21],"such":[22],"as":[23,135],"long":[24],"gene":[25,128,141,162],"lists,":[26],"or":[27],"highly":[28],"dense":[29,61],"and":[30,60,85,89,101,121,148],"overlapping":[31,62],"transcription":[32,63,114,145],"factor":[33,64,115],"networks":[34,65],"often":[35],"hinder":[36],"biologists":[37,56],"from":[38,52],"relating":[39],"these":[40],"results":[41],"to":[42,57,82,92,111,118],"their":[43,87,94],"expertise.":[44],"RESULTS:":[45],"VISIONET,":[46],"streamlined":[48],"visualisation":[49],"tool":[50],"built":[51],"experimental":[53,154,167],"needs,":[54],"enables":[55],"transform":[58],"large":[59],"into":[66],"sparse":[67],"human-readable":[68],"graphs":[69],"via":[70],"numerically":[71],"filtering.":[72],"The":[73],"VISIONET":[74,110,159],"interface":[75],"allows":[76],"users":[77],"without":[78],"computing":[80],"background":[81],"interactively":[83],"explore":[84],"filter":[86],"data,":[88],"empowers":[90],"them":[91],"apply":[93],"specialist":[95],"knowledge":[96],"on":[97],"far":[98],"more":[99],"complex":[100],"substantial":[102],"sets":[104],"than":[105],"is":[106],"currently":[107],"possible.":[108],"Applying":[109],"Tbx20-Gata4":[113],"network":[116],"led":[117],"discovery":[120,163],"validation":[122],"Aldh1a2,":[124],"an":[125],"essential":[126],"developmental":[127],"associated":[129],"with":[130,153],"various":[131],"important":[132],"cardiac":[133,139],"disorders,":[134],"healthy":[137],"adult":[138],"fibroblast":[140],"co-regulated":[142],"by":[143],"cardiogenic":[144],"factors":[146],"Gata4":[147],"Tbx20.":[149],"CONCLUSIONS:":[150],"We":[151],"demonstrate":[152],"validations":[155],"utility":[157],"for":[160],"expertise-driven":[161],"that":[164,169],"opens":[165],"new":[166],"directions":[168],"would":[170],"not":[171],"otherwise":[172],"been":[174],"identified.":[175]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
