{"id":"https://openalex.org/W2171322586","doi":"https://doi.org/10.1093/nar/gkl1041","title":"TRED: a transcriptional regulatory element database, new entries and other development","display_name":"TRED: a transcriptional regulatory element database, new entries and other development","publication_year":2007,"publication_date":"2007-01-03","ids":{"openalex":"https://openalex.org/W2171322586","doi":"https://doi.org/10.1093/nar/gkl1041","mag":"2171322586"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkl1041","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl1041","pdf_url":"https://academic.oup.com/nar/article-pdf/35/suppl_1/D137/3800059/gkl1041.pdf","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/35/suppl_1/D137/3800059/gkl1041.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005381760","display_name":"Cizhong Jiang","orcid":"https://orcid.org/0000-0001-5406-2360"},"institutions":[{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"C. Jiang","raw_affiliation_strings":["Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA","Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring HarborNY 11724, USA"],"affiliations":[{"raw_affiliation_string":"Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA","institution_ids":["https://openalex.org/I2750212522"]},{"raw_affiliation_string":"Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring HarborNY 11724, USA","institution_ids":["https://openalex.org/I2750212522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031286769","display_name":"Zhenyu Xuan","orcid":"https://orcid.org/0000-0001-9344-8493"},"institutions":[{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Z. Xuan","raw_affiliation_strings":["Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA","Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring HarborNY 11724, USA"],"affiliations":[{"raw_affiliation_string":"Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA","institution_ids":["https://openalex.org/I2750212522"]},{"raw_affiliation_string":"Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring HarborNY 11724, USA","institution_ids":["https://openalex.org/I2750212522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056366286","display_name":"Fei Zhao","orcid":"https://orcid.org/0000-0002-9087-5243"},"institutions":[{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"F. Zhao","raw_affiliation_strings":["Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA","Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring HarborNY 11724, USA"],"affiliations":[{"raw_affiliation_string":"Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA","institution_ids":["https://openalex.org/I2750212522"]},{"raw_affiliation_string":"Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring HarborNY 11724, USA","institution_ids":["https://openalex.org/I2750212522"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002023073","display_name":"M. Q. Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. Q. Zhang","raw_affiliation_strings":["Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA","Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring HarborNY 11724, USA"],"affiliations":[{"raw_affiliation_string":"Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA","institution_ids":["https://openalex.org/I2750212522"]},{"raw_affiliation_string":"Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring HarborNY 11724, USA","institution_ids":["https://openalex.org/I2750212522"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5005381760"],"corresponding_institution_ids":["https://openalex.org/I2750212522"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":5.9151,"has_fulltext":true,"cited_by_count":345,"citation_normalized_percentile":{"value":0.97180383,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"35","issue":"Database","first_page":"D137","last_page":"D140"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9962000250816345,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9962000250816345,"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/T11482","display_name":"RNA modifications and cancer","score":0.9957000017166138,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9937999844551086,"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":0.9356565475463867},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4412231743335724},{"id":"https://openalex.org/keywords/element","display_name":"Element (criminal law)","score":0.43967920541763306},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.42223870754241943},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.41841888427734375},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.07342588901519775}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.9356565475463867},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4412231743335724},{"id":"https://openalex.org/C200288055","wikidata":"https://www.wikidata.org/wiki/Q2621792","display_name":"Element (criminal law)","level":2,"score":0.43967920541763306},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.42223870754241943},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.41841888427734375},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.07342588901519775},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1093/nar/gkl1041","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl1041","pdf_url":"https://academic.oup.com/nar/article-pdf/35/suppl_1/D137/3800059/gkl1041.pdf","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmh:oai:repository.cshl.edu:23054","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402288","display_name":"Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"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":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.279.5465","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.279.5465","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/16/36/Nucleic_Acids_Res_2007_Jan_35(Database_issue)_D137-D140.tar.gz","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.577.8537","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.577.8537","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://rulai.cshl.edu/xuan/publication/TRED2007.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.579.9490","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.579.9490","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/35/suppl_1/D137.full-text-lowres.pdf","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:1899102","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1899102","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","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/gkl1041","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl1041","pdf_url":"https://academic.oup.com/nar/article-pdf/35/suppl_1/D137/3800059/gkl1041.pdf","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.4699999988079071,"id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G1140348878","display_name":null,"funder_award_id":"HG001696","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4553171568","display_name":null,"funder_award_id":"00169","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2171322586.pdf","grobid_xml":"https://content.openalex.org/works/W2171322586.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W2072775378","https://openalex.org/W2127230663","https://openalex.org/W2130919037","https://openalex.org/W2134193442","https://openalex.org/W2135030836","https://openalex.org/W2151253278","https://openalex.org/W2153392439","https://openalex.org/W2162517990","https://openalex.org/W2165460636","https://openalex.org/W4239050624"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W2151865869","https://openalex.org/W2117258802"],"abstract_inverted_index":{"Transcriptional":[0],"factors":[1],"(TFs)":[2],"and":[3,29,46,91,111,115,127,150,159],"many":[4],"of":[5,17,32,78,88,166],"their":[6,151],"target":[7,89,103,118,152],"genes":[8,92,104,153],"are":[9,100],"involved":[10,82],"in":[11,83,106,109,113,122,125,129],"gene":[12,21,44,143],"regulation":[13,45],"at":[14],"the":[15,60,67,86,141,167],"level":[16],"transcription.":[18],"To":[19],"decipher":[20],"regulatory":[22,34,61],"networks":[23],"(GRNs)":[24],"we":[25,74,132],"require":[26],"a":[27,41,76,163],"comprehensive":[28],"accurate":[30],"knowledge":[31],"transcriptional":[33],"elements.":[35],"TRED":[36],"(http://rulai.cshl.edu/TRED)":[37],"was":[38],"designed":[39],"as":[40],"resource":[42],"for":[43,93,135,169],"function":[47],"studies.":[48],"It":[49],"collects":[50],"mammalian":[51],"cis-and":[52],"trans-regulatory":[53],"elements":[54,62],"together":[55],"with":[56],"experimental":[57],"evidence.":[58],"All":[59],"were":[63],"mapped":[64],"on":[65],"to":[66,161],"assembled":[68],"genomes.":[69],"In":[70],"this":[71],"new":[72],"release,":[73],"included":[75],"total":[77],"36":[79],"TF":[80,94,137],"families":[81,95],"cancer.":[84],"Accordingly,":[85],"number":[87],"promoters":[90,119],"has":[96],"increased":[97],"dramatically.":[98],"There":[99],"11":[101],"660":[102],"(7479":[105],"human,":[107,123],"2691":[108],"mouse":[110,126],"1490":[112],"rat)":[114],"14":[116],"908":[117],"(10":[120],"225":[121],"2985":[124],"1698":[128],"rat).":[130],"Additionally,":[131],"constructed":[133],"GRNs":[134,168],"each":[136],"family":[138],"by":[139],"connecting":[140],"TF-target":[142],"pairs.":[144],"Such":[145],"interaction":[146],"data":[147],"between":[148],"TFs":[149],"will":[154],"assist":[155],"detailed":[156],"functional":[157],"studies":[158],"help":[160],"obtain":[162],"panoramic":[164],"view":[165],"cancer":[170],"research.":[171]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":16},{"year":2022,"cited_by_count":12},{"year":2021,"cited_by_count":20},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":23},{"year":2018,"cited_by_count":31},{"year":2017,"cited_by_count":20},{"year":2016,"cited_by_count":17},{"year":2015,"cited_by_count":34},{"year":2014,"cited_by_count":20},{"year":2013,"cited_by_count":27},{"year":2012,"cited_by_count":39}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
