{"id":"https://openalex.org/W2998631998","doi":"https://doi.org/10.1093/bioinformatics/btz972","title":"Differential Expression Gene Explorer (DrEdGE): a tool for generating interactive online visualizations of gene expression datasets","display_name":"Differential Expression Gene Explorer (DrEdGE): a tool for generating interactive online visualizations of gene expression datasets","publication_year":2019,"publication_date":"2019-12-31","ids":{"openalex":"https://openalex.org/W2998631998","doi":"https://doi.org/10.1093/bioinformatics/btz972","mag":"2998631998","pmid":"https://pubmed.ncbi.nlm.nih.gov/31899488","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/7178403"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz972","doi":"https://doi.org/10.1093/bioinformatics/btz972","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz972","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2019/06/10/618439.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5051962264","display_name":"Sophia Tintori","orcid":"https://orcid.org/0000-0003-0801-1700","observed_orcids":["https://orcid.org/0000-0003-0801-1700"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Sophia C Tintori","raw_affiliation_strings":["Department of Biology"],"raw_orcid":"https://orcid.org/0000-0003-0801-1700","affiliations":[{"raw_affiliation_string":"Department of Biology","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083951231","display_name":"Patrick Golden","orcid":"https://orcid.org/0000-0002-3617-9378","observed_orcids":["https://orcid.org/0000-0002-3617-9378"]},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Patrick Golden","raw_affiliation_strings":["School of Information and Library Science, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information and Library Science, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090874399","display_name":"Bob Goldstein","orcid":"https://orcid.org/0000-0001-6961-675X","observed_orcids":["https://orcid.org/0000-0001-6961-675X"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Bob Goldstein","raw_affiliation_strings":["Department of Biology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5051962264","https://openalex.org/A5090874399"],"corresponding_institution_ids":[],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.1655,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.46123276,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":97},"biblio":{"volume":"36","issue":"8","first_page":"2581","last_page":"2583"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.5443999767303467,"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/T10885","display_name":"Gene expression and cancer classification","score":0.5443999767303467,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.326200008392334,"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":0.05510000139474869,"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/differential-gene-expression","display_name":"differential gene expression","score":0.7990000247955322},{"id":"https://openalex.org/keywords/interactive-data-visualization","display_name":"interactive data visualization","score":0.7799999713897705},{"id":"https://openalex.org/keywords/web-based-visualization-tool","display_name":"web-based visualization tool","score":0.906000018119812},{"id":"https://openalex.org/keywords/exploratory-data-analysis","display_name":"exploratory data analysis","score":0.7129999995231628},{"id":"https://openalex.org/keywords/interactive-querying","display_name":"interactive querying","score":0.328000009059906}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5849330425262451},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.511987030506134},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.46671387553215027},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.4455733597278595},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.439770370721817},{"id":"https://openalex.org/C2778944004","wikidata":"https://www.wikidata.org/wiki/Q91703","display_name":"Caenorhabditis elegans","level":3,"score":0.413136750459671},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38481009006500244},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3472071886062622},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3446280360221863},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3201359510421753},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.300618439912796},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14965888857841492},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1136450469493866}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btz972","doi":"https://doi.org/10.1093/bioinformatics/btz972","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz972","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"doi:10.1101/618439","doi":"https://doi.org/10.1101/618439","is_oa":true,"landing_page_url":"https://doi.org/10.1101/618439","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2019/06/10/618439.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmh:oai:pubmedcentral.nih.gov:7178403","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7178403","pdf_url":null,"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,"listed_in":[],"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":"Bioinformatics","raw_type":"Text"},{"id":"pmid:31899488","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31899488","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,"listed_in":[],"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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1101/618439","doi":"https://doi.org/10.1101/618439","is_oa":true,"landing_page_url":"https://doi.org/10.1101/618439","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2019/06/10/618439.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1211544634","display_name":"C. elegans Gastrulation: a Model for Understanding Apical Constriction Mechanisms","funder_award_id":"R01GM083071","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2528278219","display_name":null,"funder_award_id":"R01 GM083071","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5177777326","display_name":"Using Water Bears to Investigate Adaptations to Extreme Stresses","funder_award_id":"1557432","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5520316217","display_name":null,"funder_award_id":"NIH-R01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6693247311","display_name":null,"funder_award_id":"19-1211","funder_id":"https://openalex.org/F4320306271","funder_display_name":"Damon Runyon Cancer Research Foundation"},{"id":"https://openalex.org/G9000872251","display_name":"C. elegans Gastrulation: a Model for Understanding Apical Constriction Mechanisms","funder_award_id":"R35GM134838","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306271","display_name":"Damon Runyon Cancer Research Foundation","ror":"https://ror.org/01gd7b947"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337399","display_name":"Division of Integrative Organismal Systems","ror":"https://ror.org/01rvays47"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2998631998.pdf","grobid_xml":"https://content.openalex.org/works/W2998631998.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1570863047","https://openalex.org/W1594711060","https://openalex.org/W1767470961","https://openalex.org/W2020541351","https://openalex.org/W2104549677","https://openalex.org/W2114104545","https://openalex.org/W2116041602","https://openalex.org/W2121374483","https://openalex.org/W2128016314","https://openalex.org/W2135937351","https://openalex.org/W2155301734","https://openalex.org/W2223774172","https://openalex.org/W2229672661","https://openalex.org/W2259938310","https://openalex.org/W2342688693","https://openalex.org/W2419297305","https://openalex.org/W2512439797","https://openalex.org/W2516204389","https://openalex.org/W2542446037","https://openalex.org/W2559722174","https://openalex.org/W2594490426","https://openalex.org/W2902003615","https://openalex.org/W4252710376"],"related_works":["https://openalex.org/W4282943120","https://openalex.org/W2605648435","https://openalex.org/W2766620140","https://openalex.org/W7164123067","https://openalex.org/W2129202305","https://openalex.org/W2954539166","https://openalex.org/W2569381898","https://openalex.org/W4246521269","https://openalex.org/W2750208224","https://openalex.org/W4396894255"],"abstract_inverted_index":{"Abstract":[0],"As":[1],"the":[2,20,47,129,137,146],"scientific":[3],"community":[4],"becomes":[5],"increasingly":[6],"interested":[7,142],"in":[8],"data":[9,49,63,80,147],"sharing,":[10],"there":[11],"is":[12,38],"a":[13,57,122],"growing":[14],"need":[15],"for":[16,29],"tools":[17],"that":[18,61,140],"facilitate":[19],"querying":[21],"of":[22,26,100,131],"public":[23],"data.":[24],"Mining":[25],"RNA-seq":[27],"datasets,":[28],"example,":[30],"has":[31],"value":[32],"to":[33,42,90,94],"many":[34],"biomedical":[35],"researchers,":[36],"yet":[37],"often":[39],"effectively":[40],"inaccessible":[41],"non-genomicist":[43],"experts,":[44],"even":[45],"when":[46],"raw":[48],"are":[50],"available.":[51],"Here":[52],"we":[53,110],"present":[54],"DrEdGE":[55,71,127],"(dredge.bio.unc.edu),":[56],"free":[58],"Web-based":[59],"tool":[60],"facilitates":[62],"sharing":[64],"between":[65],"genomicists":[66,74],"and":[67,87,121],"their":[68,91],"colleagues.":[69],"The":[70],"software":[72],"guides":[73],"through":[75],"easily":[76],"creating":[77],"interactive":[78],"online":[79],"visualizations,":[81],"which":[82],"colleagues":[83],"can":[84],"then":[85],"explore":[86],"query":[88],"according":[89],"own":[92],"conditions":[93],"discover":[95],"genes,":[96],"samples,":[97],"or":[98],"patterns":[99],"interest.":[101],"We":[102],"demonstrate":[103],"DrEdGE\u2019s":[104],"features":[105],"with":[106],"three":[107],"example":[108],"websites":[109],"generated":[111],"from":[112,144],"publicly":[113],"available":[114],"datasets\u2014human":[115],"neuronal":[116],"tissue,":[117,120],"mouse":[118],"embryonic":[119,125],"C.":[123],"elegans":[124],"series.":[126],"increases":[128],"utility":[130],"large":[132],"genomics":[133],"datasets":[134],"by":[135],"removing":[136],"technical":[138],"obstacles":[139],"prevent":[141],"parties":[143],"exploring":[145],"independently.":[148]},"counts_by_year":[{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":3},{"year":2020,"cited_by_count":2}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2020-01-10T00:00:00"}
