{"id":"https://openalex.org/W2082463698","doi":"https://doi.org/10.1093/nar/gkm840","title":"COXPRESdb: a database of coexpressed gene networks in mammals","display_name":"COXPRESdb: a database of coexpressed gene networks in mammals","publication_year":2007,"publication_date":"2007-10-11","ids":{"openalex":"https://openalex.org/W2082463698","doi":"https://doi.org/10.1093/nar/gkm840","mag":"2082463698","pmid":"https://pubmed.ncbi.nlm.nih.gov/17932064"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkm840","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkm840","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"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":"Nucleic Acids Research","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/nar/gkm840","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082891083","display_name":"Takeshi Obayashi","orcid":"https://orcid.org/0000-0002-3106-722X"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"T. Obayashi","raw_affiliation_strings":["Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo, Japan","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066400160","display_name":"Shinpei Hayashi","orcid":"https://orcid.org/0000-0001-7988-7772"},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"S. Hayashi","raw_affiliation_strings":["Tokyo Institute of Technology, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Tokyo Institute of Technology, Tokyo, Japan","institution_ids":["https://openalex.org/I114531698"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024150802","display_name":"Masayuki Shibaoka","orcid":null},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"M. Shibaoka","raw_affiliation_strings":["Tokyo Institute of Technology, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Tokyo Institute of Technology, Tokyo, Japan","institution_ids":["https://openalex.org/I114531698"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018583174","display_name":"Motoshi Saeki","orcid":null},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"M. Saeki","raw_affiliation_strings":["Tokyo Institute of Technology, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Tokyo Institute of Technology, Tokyo, Japan","institution_ids":["https://openalex.org/I114531698"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091691483","display_name":"Hiroyuki Ohta","orcid":"https://orcid.org/0000-0002-1068-3242"},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"H. Ohta","raw_affiliation_strings":["Tokyo Institute of Technology, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Tokyo Institute of Technology, Tokyo, Japan","institution_ids":["https://openalex.org/I114531698"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113923031","display_name":"Kiyoshi Kinoshita","orcid":null},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"K. Kinoshita","raw_affiliation_strings":["Tokyo Institute of Technology, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Tokyo Institute of Technology, Tokyo, Japan","institution_ids":["https://openalex.org/I114531698"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5082891083"],"corresponding_institution_ids":[],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":4.4371,"has_fulltext":false,"cited_by_count":183,"citation_normalized_percentile":{"value":0.95388612,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"36","issue":"Database","first_page":"D77","last_page":"D82"},"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/T10885","display_name":"Gene expression and cancer classification","score":0.9986000061035156,"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/T10604","display_name":"RNA Research and Splicing","score":0.9904999732971191,"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/biology","display_name":"Biology","score":0.8803056478500366},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.7708251476287842},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.6291602253913879},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5533982515335083},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5327553749084473},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4544749855995178},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2862236201763153},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.06222081184387207}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8803056478500366},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.7708251476287842},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.6291602253913879},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5533982515335083},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5327553749084473},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4544749855995178},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2862236201763153},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.06222081184387207}],"mesh":[{"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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","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":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051378","descriptor_name":"Actin-Related Protein 3","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D051378","descriptor_name":"Actin-Related Protein 3","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D051378","descriptor_name":"Actin-Related Protein 3","qualifier_ui":"Q000235","qualifier_name":"genetics","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},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"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}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gkm840","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkm840","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:17932064","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17932064","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.283.4957","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.283.4957","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/61/58/Nucleic_Acids_Res_2008_Jan_36(Database_issue)_D77-D82.tar.gz","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:2238883","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2238883","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkm840","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkm840","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.6600000262260437,"id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G12401395","display_name":null,"funder_award_id":"Technology","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G7599130655","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G7693551792","display_name":null,"funder_award_id":"(MEXT)","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G8044579487","display_name":null,"funder_award_id":"Japan","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"},{"id":"https://openalex.org/F4320322832","display_name":"University of Tokyo","ror":"https://ror.org/057zh3y96"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1954784702","https://openalex.org/W2001457899","https://openalex.org/W2014978570","https://openalex.org/W2022756254","https://openalex.org/W2048368626","https://openalex.org/W2065716803","https://openalex.org/W2066299394","https://openalex.org/W2083737836","https://openalex.org/W2096525273","https://openalex.org/W2100471807","https://openalex.org/W2103017472","https://openalex.org/W2115111790","https://openalex.org/W2133747068","https://openalex.org/W2134187096","https://openalex.org/W2134672568","https://openalex.org/W2136067601","https://openalex.org/W2150926065","https://openalex.org/W2154362705","https://openalex.org/W2157815908","https://openalex.org/W2158173168","https://openalex.org/W2165674132","https://openalex.org/W2170989872","https://openalex.org/W4245543257"],"related_works":["https://openalex.org/W2003932708","https://openalex.org/W2138102289","https://openalex.org/W1967424056","https://openalex.org/W868043274","https://openalex.org/W2513523087","https://openalex.org/W1187916458","https://openalex.org/W2373861055","https://openalex.org/W1559716973","https://openalex.org/W3109364360","https://openalex.org/W2034625591"],"abstract_inverted_index":{"A":[0],"database":[1],"of":[2,14,20,106,110],"coexpressed":[3,69,115],"gene":[4,25,31,65,70,137],"sets":[5],"can":[6],"provide":[7],"valuable":[8],"information":[9],"for":[10,22,50,68,83,117,145],"a":[11,60,171],"wide":[12],"variety":[13],"experimental":[15],"designs,":[16],"such":[17],"as":[18],"targeting":[19],"genes":[21,89,116,121,128],"functional":[23],"identification,":[24],"regulation":[26],"and/or":[27],"protein-protein":[28],"interactions.":[29],"Coexpressed":[30],"databases":[32],"derived":[33],"from":[34],"publicly":[35],"available":[36],"GeneChip":[37,98],"data":[38,79,99],"are":[39,53],"widely":[40],"used":[41,160],"in":[42,74,90,100,130,152,156],"Arabidopsis":[43],"research,":[44],"but":[45],"platforms":[46],"that":[47],"examine":[48],"coexpression":[49,111,179],"higher":[51],"mammals":[52],"rather":[54],"limited.":[55],"Therefore,":[56],"we":[57,159],"have":[58],"constructed":[59],"new":[61],"database,":[62],"COXPRESdb":[63,103,168],"(coexpressed":[64],"database)":[66],"(http://coxpresdb.hgc.jp),":[67],"lists":[71],"and":[72,76,86,92,134,177],"networks":[73,141,154],"human":[75,91,176],"mouse.":[77],"Coexpression":[78],"could":[80],"be":[81],"calculated":[82],"19":[84],"777":[85],"21":[87],"036":[88],"mouse,":[93],"respectively,":[94],"by":[95],"using":[96],"the":[97,107,123,131,140,146,150,175,183,186],"NCBI":[101],"GEO.":[102],"enables":[104],"analysis":[105],"four":[108],"types":[109],"networks:":[112],"(i)":[113],"highly":[114],"every":[118],"gene,":[119],"(ii)":[120],"with":[122],"same":[124,132],"GO":[125,153],"annotation,":[126],"(iii)":[127],"expressed":[129],"tissue":[133,157],"(iv)":[135],"user-defined":[136],"sets.":[138],"When":[139],"became":[142],"too":[143],"big":[144],"static":[147],"picture":[148],"on":[149],"web":[151],"or":[155],"networks,":[158],"Google":[161],"Maps":[162],"API":[163],"to":[164,173,181],"visualize":[165],"them":[166],"interactively.":[167],"also":[169],"provides":[170],"view":[172],"compare":[174],"mouse":[178],"patterns":[180],"estimate":[182],"conservation":[184],"between":[185],"two":[187],"species.":[188]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":40},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":10},{"year":2014,"cited_by_count":13},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":18}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
