{"id":"https://openalex.org/W4239050624","doi":"https://doi.org/10.1093/nar/gkj129","title":"DBTSS: DataBase of Human Transcription Start Sites, progress report 2006","display_name":"DBTSS: DataBase of Human Transcription Start Sites, progress report 2006","publication_year":2005,"publication_date":"2005-12-28","ids":{"openalex":"https://openalex.org/W4239050624","doi":"https://doi.org/10.1093/nar/gkj129","pmid":"https://pubmed.ncbi.nlm.nih.gov/16381981"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkj129","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj129","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D86/3926042/gkj129.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","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D86/3926042/gkj129.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101697566","display_name":"Riu Yamashita","orcid":"https://orcid.org/0000-0003-0068-6949"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]},{"id":"https://openalex.org/I161296585","display_name":"Tokyo University of Science","ror":"https://ror.org/05sj3n476","country_code":"JP","type":"education","lineage":["https://openalex.org/I161296585"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"R. Yamashita","raw_affiliation_strings":["Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan","Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan and"],"affiliations":[{"raw_affiliation_string":"Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan","institution_ids":["https://openalex.org/I74801974","https://openalex.org/I161296585"]},{"raw_affiliation_string":"Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan and","institution_ids":["https://openalex.org/I74801974","https://openalex.org/I161296585"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5101697566"],"corresponding_institution_ids":["https://openalex.org/I161296585","https://openalex.org/I74801974"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":6.5824,"has_fulltext":true,"cited_by_count":80,"citation_normalized_percentile":{"value":0.97632732,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"34","issue":"90001","first_page":"D86","last_page":"D89"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9908999800682068,"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":0.9908999800682068,"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":0.9876999855041504,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9810000061988831,"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":0.8962689638137817},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.8678027391433716},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6838911771774292},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.5868399143218994},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5435556769371033},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46861132979393005},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2603413462638855}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8962689638137817},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.8678027391433716},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6838911771774292},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.5868399143218994},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5435556769371033},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46861132979393005},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2603413462638855},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000461","descriptor_name":"Rhodophyta","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000461","descriptor_name":"Rhodophyta","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000461","descriptor_name":"Rhodophyta","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"D010963","descriptor_name":"Plasmodium falciparum","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010963","descriptor_name":"Plasmodium falciparum","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010963","descriptor_name":"Plasmodium falciparum","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":"D015027","descriptor_name":"Zebrafish","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015027","descriptor_name":"Zebrafish","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015027","descriptor_name":"Zebrafish","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","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":5,"locations":[{"id":"doi:10.1093/nar/gkj129","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj129","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D86/3926042/gkj129.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":"pmid:16381981","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16381981","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:10.1.1.105.9467","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.105.9467","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/34/suppl_1/D86.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.275.9948","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.275.9948","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/c7/29/Nucleic_Acids_Res_2006_Jan_1_34(Database_issue)_D86-D89.tar.gz","raw_type":"text"},{"id":"pmh:oai:europepmc.org:156919","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1347491","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkj129","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj129","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D86/3926042/gkj129.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":[{"score":0.5199999809265137,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"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/G168519638","display_name":null,"funder_award_id":"special","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G3538276699","display_name":null,"funder_award_id":"Scientific_Research_on_Priority","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G6267471473","display_name":null,"funder_award_id":"Grant-in-Aid","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/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/F4320336716","display_name":"Institute of Medical Science, University of Tokyo","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4239050624.pdf","grobid_xml":"https://content.openalex.org/works/W4239050624.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W189143987","https://openalex.org/W1972875048","https://openalex.org/W1973931828","https://openalex.org/W1986234964","https://openalex.org/W2021342194","https://openalex.org/W2026726511","https://openalex.org/W2032284355","https://openalex.org/W2034102836","https://openalex.org/W2049303243","https://openalex.org/W2056839029","https://openalex.org/W2084847549","https://openalex.org/W2100278941","https://openalex.org/W2118151959","https://openalex.org/W2136785696","https://openalex.org/W2138197117","https://openalex.org/W2155530972","https://openalex.org/W2162304711","https://openalex.org/W4213167074"],"related_works":["https://openalex.org/W1969771092","https://openalex.org/W2025529750","https://openalex.org/W2891858816","https://openalex.org/W184057646","https://openalex.org/W2042874675","https://openalex.org/W3212414177","https://openalex.org/W129398428","https://openalex.org/W1975811142","https://openalex.org/W2034625591","https://openalex.org/W2139566393"],"abstract_inverted_index":{"DBTSS":[0,99,123],"was":[1],"first":[2],"constructed":[3],"in":[4],"2002":[5],"based":[6],"on":[7],"precise,":[8],"experimentally":[9],"determined":[10],"5'":[11,52],"end":[12,53],"clones.":[13],"Several":[14],"major":[15],"updates":[16],"and":[17,87,116],"additions":[18],"have":[19,94,109],"been":[20],"made":[21],"since":[22],"the":[23,27,49],"last":[24],"report.":[25],"First,":[26],"number":[28,50],"of":[29,51,83,104],"human":[30,85],"clones":[31,54],"has":[32],"drastically":[33],"increased,":[34],"going":[35],"from":[36],"190,964":[37],"to":[38,58,93],"1,359,000.":[39],"Second,":[40],"information":[41,112],"about":[42],"potential":[43],"alternative":[44],"promoters":[45,61],"is":[46,55,124],"presented":[47],"because":[48],"now":[56],"sufficient":[57],"determine":[59],"several":[60],"for":[62,113],"one":[63],"gene.":[64],"Namely,":[65],"we":[66,108],"defined":[67],"putative":[68,95],"promoter":[69],"groups":[70],"by":[71,78],"clustering":[72],"transcription":[73],"start":[74],"sites":[75],"(TSSs)":[76],"separated":[77],"<500":[79],"bases.":[80],"A":[81],"total":[82],"8308":[84],"genes":[86,90],"4276":[88],"mouse":[89],"were":[91],"found":[92],"multiple":[96],"promoters.":[97],"Third,":[98],"provides":[100],"detailed":[101],"sequence":[102],"comparisons":[103],"user-specified":[105],"TSSs.":[106],"Finally,":[107],"added":[110],"TSS":[111],"zebrafish,":[114],"malaria":[115],"schyzon":[117],"(a":[118],"red":[119],"algae":[120],"model":[121],"organism).":[122],"accessible":[125],"at":[126],"http://dbtss.hgc.jp.":[127]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2014,"cited_by_count":4},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
