{"id":"https://openalex.org/W2072775378","doi":"https://doi.org/10.1093/nar/gki004","title":"TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies","display_name":"TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies","publication_year":2004,"publication_date":"2004-12-17","ids":{"openalex":"https://openalex.org/W2072775378","doi":"https://doi.org/10.1093/nar/gki004","mag":"2072775378","pmid":"https://pubmed.ncbi.nlm.nih.gov/15608156"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gki004","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki004","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_1/D103/7621396/gki004.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":false,"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","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/nar/article-pdf/33/suppl_1/D103/7621396/gki004.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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":true,"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 Harbor, NY, 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 Harbor, NY, 11724, USA","institution_ids":["https://openalex.org/I2750212522"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5056366286"],"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":3.6175,"has_fulltext":true,"cited_by_count":201,"citation_normalized_percentile":{"value":0.93499702,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"33","issue":"Database issue","first_page":"D103","last_page":"D107"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","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/T10222","display_name":"Genomics and Chromatin Dynamics","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/T10604","display_name":"RNA Research and Splicing","score":0.9987999796867371,"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":0.9986000061035156,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7793161869049072},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6310651302337646},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.6144191026687622},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5881780385971069},{"id":"https://openalex.org/keywords/transcriptional-regulation","display_name":"Transcriptional regulation","score":0.5865797400474548},{"id":"https://openalex.org/keywords/decipher","display_name":"DECIPHER","score":0.5670524835586548},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5559520721435547},{"id":"https://openalex.org/keywords/regulatory-sequence","display_name":"Regulatory sequence","score":0.5535364151000977},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5523751378059387},{"id":"https://openalex.org/keywords/cis-regulatory-module","display_name":"Cis-regulatory module","score":0.512654721736908},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4606179893016815},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.44357287883758545},{"id":"https://openalex.org/keywords/gene-annotation","display_name":"Gene Annotation","score":0.43554043769836426},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.406653493642807},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.38595718145370483},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.329915851354599},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.19778713583946228},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.15307456254959106}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7793161869049072},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6310651302337646},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.6144191026687622},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5881780385971069},{"id":"https://openalex.org/C27153228","wikidata":"https://www.wikidata.org/wiki/Q3787274","display_name":"Transcriptional regulation","level":4,"score":0.5865797400474548},{"id":"https://openalex.org/C164614171","wikidata":"https://www.wikidata.org/wiki/Q5204775","display_name":"DECIPHER","level":2,"score":0.5670524835586548},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5559520721435547},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.5535364151000977},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5523751378059387},{"id":"https://openalex.org/C190796033","wikidata":"https://www.wikidata.org/wiki/Q1093165","display_name":"Cis-regulatory module","level":5,"score":0.512654721736908},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4606179893016815},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.44357287883758545},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.43554043769836426},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.406653493642807},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.38595718145370483},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.329915851354599},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.19778713583946228},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.15307456254959106}],"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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"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},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/nar/gki004","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki004","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_1/D103/7621396/gki004.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":false,"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":"pmid:15608156","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15608156","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:repository.cshl.edu:22743","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":"Paper"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.956.3066","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.956.3066","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/33/suppl_1/D103.full.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.96.993","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.96.993","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/cgi/reprint/33/suppl_1/D103.pdf","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:539958","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/539958","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/gki004","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki004","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_1/D103/7621396/gki004.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":false,"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":[],"awards":[{"id":"https://openalex.org/G1027002839","display_name":null,"funder_award_id":"HG01696","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"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2072775378.pdf","grobid_xml":"https://content.openalex.org/works/W2072775378.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1214546200","https://openalex.org/W1976334162","https://openalex.org/W1981805884","https://openalex.org/W1994017531","https://openalex.org/W1998300401","https://openalex.org/W2017200304","https://openalex.org/W2083479872","https://openalex.org/W2084620487","https://openalex.org/W2101690350","https://openalex.org/W2101904615","https://openalex.org/W2130919037","https://openalex.org/W2132786809","https://openalex.org/W2138974722","https://openalex.org/W2143550361","https://openalex.org/W2160014402","https://openalex.org/W2166898290","https://openalex.org/W2168459422","https://openalex.org/W4213167074","https://openalex.org/W4242043490"],"related_works":["https://openalex.org/W2153800196","https://openalex.org/W2117549173","https://openalex.org/W2598257048","https://openalex.org/W2184089867","https://openalex.org/W2947121614","https://openalex.org/W184373668","https://openalex.org/W1991485331","https://openalex.org/W1564684180","https://openalex.org/W2917003957","https://openalex.org/W2136726922"],"abstract_inverted_index":{"In":[0],"order":[1],"to":[2,44],"understand":[3],"gene":[4,75,136],"regulation,":[5],"accurate":[6],"and":[7,38,41,48,53,70,84,101,105,125,131],"comprehensive":[8],"knowledge":[9],"of":[10,58,74,108,135],"transcriptional":[11,76],"regulatory":[12,137],"elements":[13,40],"is":[14,42,90],"essential.":[15],"Here,":[16],"we":[17],"report":[18],"our":[19],"efforts":[20],"in":[21],"building":[22],"a":[23],"mammalian":[24],"Transcriptional":[25],"Regulatory":[26],"Element":[27],"Database":[28],"(TRED)":[29],"with":[30],"associated":[31],"data":[32,46,88,103],"analysis":[33,49,111],"functions.":[34],"It":[35],"collects":[36],"cis-":[37],"trans-regulatory":[39],"dedicated":[43],"easy":[45,100],"access":[47],"for":[50,67,99,119],"both":[51],"single-gene-based":[52],"genome-scale":[54],"studies.":[55],"Distinguishing":[56],"features":[57],"TRED":[59,113],"include:":[60],"(i)":[61],"relatively":[62],"complete":[63],"genome-wide":[64,121],"promoter":[65],"annotation":[66],"human,":[68],"mouse":[69],"rat;":[71],"(ii)":[72],"availability":[73],"regulation":[77],"information":[78],"including":[79],"transcription":[80],"factor":[81],"binding":[82],"sites":[83],"experimental":[85],"evidence;":[86],"(iii)":[87],"accuracy":[89],"ensured":[91],"by":[92],"hand":[93],"curation;":[94],"(iv)":[95],"efficient":[96],"user":[97],"interface":[98],"flexible":[102],"retrieval;":[104],"(v)":[106],"implementation":[107],"on-the-fly":[109],"sequence":[110],"tools.":[112],"can":[114],"provide":[115],"good":[116],"training":[117],"datasets":[118],"further":[120],"cis-regulatory":[122],"element":[123],"prediction":[124],"annotation,":[126],"assist":[127],"detailed":[128],"functional":[129],"studies":[130],"facilitate":[132],"the":[133],"decipher":[134],"networks":[138],"(http://rulai.cshl.edu/TRED).":[139]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":13},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":10},{"year":2017,"cited_by_count":14},{"year":2016,"cited_by_count":10},{"year":2015,"cited_by_count":14},{"year":2014,"cited_by_count":18},{"year":2013,"cited_by_count":17},{"year":2012,"cited_by_count":16}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
