{"id":"https://openalex.org/W2931036699","doi":"https://doi.org/10.1093/database/baz046","title":"PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data","display_name":"PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data","publication_year":2019,"publication_date":"2019-01-01","ids":{"openalex":"https://openalex.org/W2931036699","doi":"https://doi.org/10.1093/database/baz046","mag":"2931036699","pmid":"https://pubmed.ncbi.nlm.nih.gov/30951143"},"language":"en","primary_location":{"id":"doi:10.1093/database/baz046","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baz046","pdf_url":null,"source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/database/baz046","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026869903","display_name":"Oscar Franz\u00e9n","orcid":"https://orcid.org/0000-0002-7573-0812"},"institutions":[{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]},{"id":"https://openalex.org/I4210105493","display_name":"Integrated Cardio Metabolic Centre","ror":"https://ror.org/01pgex273","country_code":"SE","type":"facility","lineage":["https://openalex.org/I105036370","https://openalex.org/I28166907","https://openalex.org/I4210105493","https://openalex.org/I4210143795"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Oscar Franz\u00e9n","raw_affiliation_strings":["Integrated Cardio Metabolic Centre (ICMC), Department of Medicine, Karolinska Institutet, Novum SE Huddinge, Sweden"],"raw_orcid":"https://orcid.org/0000-0002-7573-0812","affiliations":[{"raw_affiliation_string":"Integrated Cardio Metabolic Centre (ICMC), Department of Medicine, Karolinska Institutet, Novum SE Huddinge, Sweden","institution_ids":["https://openalex.org/I4210105493","https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101664119","display_name":"Li\u2010Ming Gan","orcid":"https://orcid.org/0000-0003-2933-1404"},"institutions":[{"id":"https://openalex.org/I4210143795","display_name":"AstraZeneca (Sweden)","ror":"https://ror.org/04wwrrg31","country_code":"SE","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210143795"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Li-Ming Gan","raw_affiliation_strings":["Cardiovascular, Renal and Metabolism Translational Medicines Unit, Early Clinical Development, IMED Biotech Unit, AstraZeneca, Pepparedsleden, M\u00f6lndal, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cardiovascular, Renal and Metabolism Translational Medicines Unit, Early Clinical Development, IMED Biotech Unit, AstraZeneca, Pepparedsleden, M\u00f6lndal, Sweden","institution_ids":["https://openalex.org/I4210143795"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067811406","display_name":"Johan Bj\u00f6rkegren","orcid":"https://orcid.org/0000-0003-1945-7425"},"institutions":[{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]},{"id":"https://openalex.org/I4210105493","display_name":"Integrated Cardio Metabolic Centre","ror":"https://ror.org/01pgex273","country_code":"SE","type":"facility","lineage":["https://openalex.org/I105036370","https://openalex.org/I28166907","https://openalex.org/I4210105493","https://openalex.org/I4210143795"]},{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["SE","US"],"is_corresponding":false,"raw_author_name":"Johan L M Bj\u00f6rkegren","raw_affiliation_strings":["Icahn Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA","Integrated Cardio Metabolic Centre (ICMC), Department of Medicine, Karolinska Institutet, Novum SE Huddinge, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Icahn Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA","institution_ids":["https://openalex.org/I98704320"]},{"raw_affiliation_string":"Integrated Cardio Metabolic Centre (ICMC), Department of Medicine, Karolinska Institutet, Novum SE Huddinge, Sweden","institution_ids":["https://openalex.org/I4210105493","https://openalex.org/I28166907"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5026869903"],"corresponding_institution_ids":["https://openalex.org/I28166907","https://openalex.org/I4210105493"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":44.1925,"has_fulltext":false,"cited_by_count":1669,"citation_normalized_percentile":{"value":0.99923438,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"2019","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.989300012588501,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9872000217437744,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/computer-science","display_name":"Computer science","score":0.6152043342590332},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5320205688476562},{"id":"https://openalex.org/keywords/cell-type","display_name":"Cell type","score":0.5238218903541565},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5060989260673523},{"id":"https://openalex.org/keywords/compendium","display_name":"Compendium","score":0.4774251878261566},{"id":"https://openalex.org/keywords/cell","display_name":"Cell","score":0.47699692845344543},{"id":"https://openalex.org/keywords/single-cell-analysis","display_name":"Single-cell analysis","score":0.4564710557460785},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.4525517523288727},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.33731287717819214},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.30740025639533997},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.21327939629554749},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16826856136322021},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.11535894870758057}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6152043342590332},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5320205688476562},{"id":"https://openalex.org/C189014844","wikidata":"https://www.wikidata.org/wiki/Q189118","display_name":"Cell type","level":3,"score":0.5238218903541565},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5060989260673523},{"id":"https://openalex.org/C2778473407","wikidata":"https://www.wikidata.org/wiki/Q1459574","display_name":"Compendium","level":2,"score":0.4774251878261566},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.47699692845344543},{"id":"https://openalex.org/C2776950831","wikidata":"https://www.wikidata.org/wiki/Q15635432","display_name":"Single-cell analysis","level":3,"score":0.4564710557460785},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.4525517523288727},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.33731287717819214},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30740025639533997},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.21327939629554749},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16826856136322021},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.11535894870758057},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"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":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","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},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/database/baz046","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baz046","pdf_url":null,"source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},{"id":"pmid:30951143","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30951143","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:europepmc.org:5438763","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6450036","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6450036","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6450036","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,"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":"Database (Oxford)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/baz046","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baz046","pdf_url":null,"source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.46000000834465027,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G8470748440","display_name":null,"funder_award_id":"2018-02529","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"}],"funders":[{"id":"https://openalex.org/F4320322315","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691"},{"id":"https://openalex.org/F4320322581","display_name":"Vetenskapsr\u00e5det","ror":"https://ror.org/03zttf063"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W1580018887","https://openalex.org/W1966327575","https://openalex.org/W1989800873","https://openalex.org/W2020541351","https://openalex.org/W2032578973","https://openalex.org/W2033169664","https://openalex.org/W2067899297","https://openalex.org/W2068767807","https://openalex.org/W2076513103","https://openalex.org/W2084942072","https://openalex.org/W2096465161","https://openalex.org/W2102212449","https://openalex.org/W2102278945","https://openalex.org/W2105389823","https://openalex.org/W2107281049","https://openalex.org/W2108234281","https://openalex.org/W2110065044","https://openalex.org/W2110905563","https://openalex.org/W2116041602","https://openalex.org/W2128505445","https://openalex.org/W2129099812","https://openalex.org/W2140952049","https://openalex.org/W2161849959","https://openalex.org/W2176034226","https://openalex.org/W2187089797","https://openalex.org/W2214074259","https://openalex.org/W2338756998","https://openalex.org/W2516455020","https://openalex.org/W2540833380","https://openalex.org/W2547834322","https://openalex.org/W2573731673","https://openalex.org/W2616922646","https://openalex.org/W2744684750","https://openalex.org/W2750304043","https://openalex.org/W2765472239","https://openalex.org/W2770178180","https://openalex.org/W2775437905","https://openalex.org/W2786672974","https://openalex.org/W2794480084","https://openalex.org/W2895456557","https://openalex.org/W2901292166","https://openalex.org/W2952109315","https://openalex.org/W6728888212","https://openalex.org/W6729469731","https://openalex.org/W6748816842"],"related_works":["https://openalex.org/W2164288075","https://openalex.org/W2384167225","https://openalex.org/W2113182373","https://openalex.org/W4255195499","https://openalex.org/W2088998312","https://openalex.org/W2312055187","https://openalex.org/W2965166405","https://openalex.org/W4283385293","https://openalex.org/W3137609122","https://openalex.org/W4315474746"],"abstract_inverted_index":{"Single-cell":[0],"RNA":[1,83],"sequencing":[2,26,84],"is":[3],"an":[4,62],"increasingly":[5],"used":[6,74],"method":[7],"to":[8,43,49,75,126],"measure":[9],"gene":[10],"expression":[11],"at":[12],"the":[13,50],"single":[14,81,101],"cell":[15,82,102,130,160],"level":[16],"and":[17,79,89,104,119,128,134],"build":[18],"cell-type":[19,144],"atlases":[20],"of":[21,24,117,159],"tissues.":[22],"Hundreds":[23],"single-cell":[25,96],"datasets":[27],"have":[28,60,140],"already":[29],"been":[30],"published.":[31],"However,":[32],"studies":[33],"are":[34],"frequently":[35],"deposited":[36],"as":[37,153],"raw":[38],"data,":[39],"a":[40,68,114,142,154],"format":[41],"difficult":[42],"access":[44],"for":[45,52,156],"biological":[46],"researchers":[47],"due":[48],"need":[51],"data":[53],"processing":[54],"using":[55],"complex":[56],"computational":[57],"pipelines.":[58],"We":[59],"implemented":[61],"online":[63,122],"database,":[64],"PanglaoDB,":[65],"accessible":[66],"through":[67],"user-friendly":[69],"interface":[70,123],"that":[71],"can":[72],"be":[73],"explore":[76,129],"published":[77],"mouse":[78],"human":[80],"studies.":[85],"PanglaoDB":[86],"contains":[87],"pre-processed":[88],"pre-computed":[90],"analyses":[91],"from":[92,113],"more":[93,108,148],"than":[94,109,149],"1054":[95],"experiments":[97],"covering":[98],"most":[99],"major":[100],"platforms":[103],"protocols,":[105],"based":[106],"on":[107],"4":[110],"million":[111],"cells":[112],"wide":[115],"range":[116],"tissues":[118],"organs.":[120],"The":[121],"allows":[124],"users":[125],"query":[127],"types,":[131],"genetic":[132],"pathways":[133],"regulatory":[135],"networks.":[136],"In":[137],"addition,":[138],"we":[139],"established":[141],"community-curated":[143],"marker":[145],"compendium,":[146],"containing":[147],"6000":[150],"gene-cell-type":[151],"associations,":[152],"resource":[155],"automatic":[157],"annotation":[158],"types.":[161]},"counts_by_year":[{"year":2026,"cited_by_count":137},{"year":2025,"cited_by_count":348},{"year":2024,"cited_by_count":365},{"year":2023,"cited_by_count":306},{"year":2022,"cited_by_count":235},{"year":2021,"cited_by_count":169},{"year":2020,"cited_by_count":95},{"year":2019,"cited_by_count":13},{"year":2018,"cited_by_count":1}],"updated_date":"2026-06-19T17:40:00.097472","created_date":"2025-10-10T00:00:00"}
