{"id":"https://openalex.org/W2031028431","doi":"https://doi.org/10.1186/1471-2105-8-161","title":"Large-scale clustering of CAGE tag expression data","display_name":"Large-scale clustering of CAGE tag expression data","publication_year":2007,"publication_date":"2007-05-21","ids":{"openalex":"https://openalex.org/W2031028431","doi":"https://doi.org/10.1186/1471-2105-8-161","mag":"2031028431","pmid":"https://pubmed.ncbi.nlm.nih.gov/17517134"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-8-161","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-161","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-161","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-161","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102901825","display_name":"Kazuro Shimokawa","orcid":"https://orcid.org/0000-0002-6707-2856"},"institutions":[{"id":"https://openalex.org/I4210150921","display_name":"RIKEN Center for Integrative Medical Sciences","ror":"https://ror.org/04mb6s476","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210150921"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Kazuro Shimokawa","raw_affiliation_strings":["Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan. kazsi@gsc.riken.jp","Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan. kazsi@gsc.riken.jp","institution_ids":["https://openalex.org/I4210150921"]},{"raw_affiliation_string":"Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan","institution_ids":["https://openalex.org/I4210150921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041443588","display_name":"Yuko Okamura-Oho","orcid":"https://orcid.org/0000-0002-2066-407X"},"institutions":[{"id":"https://openalex.org/I4210150921","display_name":"RIKEN Center for Integrative Medical Sciences","ror":"https://ror.org/04mb6s476","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210150921"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yuko Okamura-Oho","raw_affiliation_strings":["Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan","institution_ids":["https://openalex.org/I4210150921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086456461","display_name":"Takio Kurita","orcid":"https://orcid.org/0000-0003-3982-6750"},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takio Kurita","raw_affiliation_strings":["National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, 305-8568, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, 305-8568, Japan","institution_ids":["https://openalex.org/I73613424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055829507","display_name":"Martin C. Frith","orcid":"https://orcid.org/0000-0003-0998-2859"},"institutions":[{"id":"https://openalex.org/I4210150921","display_name":"RIKEN Center for Integrative Medical Sciences","ror":"https://ror.org/04mb6s476","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210150921"]},{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU","JP"],"is_corresponding":false,"raw_author_name":"Martin C Frith","raw_affiliation_strings":["Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan","Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld, 4072, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan","institution_ids":["https://openalex.org/I4210150921"]},{"raw_affiliation_string":"Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld, 4072, Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068559343","display_name":"Jun Kawai","orcid":"https://orcid.org/0000-0002-1289-7666"},"institutions":[{"id":"https://openalex.org/I110220311","display_name":"Wako University","ror":"https://ror.org/05n7t1e46","country_code":"JP","type":"education","lineage":["https://openalex.org/I110220311"]},{"id":"https://openalex.org/I4210110652","display_name":"RIKEN","ror":"https://ror.org/01sjwvz98","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652"]},{"id":"https://openalex.org/I4210150921","display_name":"RIKEN Center for Integrative Medical Sciences","ror":"https://ror.org/04mb6s476","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210150921"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Jun Kawai","raw_affiliation_strings":["Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan","Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan","institution_ids":["https://openalex.org/I4210150921"]},{"raw_affiliation_string":"Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan","institution_ids":["https://openalex.org/I110220311","https://openalex.org/I4210110652"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072131150","display_name":"Piero Carninci","orcid":"https://orcid.org/0000-0001-7202-7243"},"institutions":[{"id":"https://openalex.org/I110220311","display_name":"Wako University","ror":"https://ror.org/05n7t1e46","country_code":"JP","type":"education","lineage":["https://openalex.org/I110220311"]},{"id":"https://openalex.org/I4210110652","display_name":"RIKEN","ror":"https://ror.org/01sjwvz98","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652"]},{"id":"https://openalex.org/I4210150921","display_name":"RIKEN Center for Integrative Medical Sciences","ror":"https://ror.org/04mb6s476","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210150921"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Piero Carninci","raw_affiliation_strings":["Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan","Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan","institution_ids":["https://openalex.org/I4210150921"]},{"raw_affiliation_string":"Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan","institution_ids":["https://openalex.org/I110220311","https://openalex.org/I4210110652"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032097008","display_name":"Yoshihide Hayashizaki","orcid":"https://orcid.org/0000-0002-0561-2802"},"institutions":[{"id":"https://openalex.org/I4210150921","display_name":"RIKEN Center for Integrative Medical Sciences","ror":"https://ror.org/04mb6s476","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210150921"]},{"id":"https://openalex.org/I4210110652","display_name":"RIKEN","ror":"https://ror.org/01sjwvz98","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652"]},{"id":"https://openalex.org/I110220311","display_name":"Wako University","ror":"https://ror.org/05n7t1e46","country_code":"JP","type":"education","lineage":["https://openalex.org/I110220311"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yoshihide Hayashizaki","raw_affiliation_strings":["Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan","Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan","institution_ids":["https://openalex.org/I4210150921"]},{"raw_affiliation_string":"Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan","institution_ids":["https://openalex.org/I110220311","https://openalex.org/I4210110652"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5102901825"],"corresponding_institution_ids":["https://openalex.org/I4210150921"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.4037,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.62111221,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"8","issue":"1","first_page":"161","last_page":"161"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.5867999792098999,"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":0.5867999792098999,"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":0.1501999944448471,"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":0.017999999225139618,"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/hierarchical-clustering","display_name":"Hierarchical clustering","score":0.7588552236557007},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6786335706710815},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5624496936798096},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5490522384643555},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5018863677978516},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.46489185094833374},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4458172023296356},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.42585238814353943},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.40204840898513794},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.40070056915283203},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.3311915695667267},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22982120513916016},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19461417198181152}],"concepts":[{"id":"https://openalex.org/C92835128","wikidata":"https://www.wikidata.org/wiki/Q1277447","display_name":"Hierarchical clustering","level":3,"score":0.7588552236557007},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6786335706710815},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5624496936798096},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5490522384643555},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5018863677978516},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.46489185094833374},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4458172023296356},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.42585238814353943},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.40204840898513794},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40070056915283203},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3311915695667267},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22982120513916016},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19461417198181152},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","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}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-8-161","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-161","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-161","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:17517134","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17517134","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:dd3677e8b4664761967643399ca1420b","is_oa":false,"landing_page_url":"https://doaj.org/article/dd3677e8b4664761967643399ca1420b","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 8, Iss 1, p 161 (2007)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:1424007","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1890301","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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-8-161","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-161","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-161","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"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/F4320335125","display_name":"RIKEN","ror":"https://ror.org/01sjwvz98"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2031028431.pdf","grobid_xml":"https://content.openalex.org/works/W2031028431.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W69605169","https://openalex.org/W1489980839","https://openalex.org/W1618318544","https://openalex.org/W1840933474","https://openalex.org/W1970156673","https://openalex.org/W1975658784","https://openalex.org/W1983751803","https://openalex.org/W1986234964","https://openalex.org/W2002982210","https://openalex.org/W2003668590","https://openalex.org/W2010888033","https://openalex.org/W2016927884","https://openalex.org/W2023180113","https://openalex.org/W2046550890","https://openalex.org/W2047796164","https://openalex.org/W2053150867","https://openalex.org/W2057692691","https://openalex.org/W2059496903","https://openalex.org/W2099468911","https://openalex.org/W2099600000","https://openalex.org/W2105860794","https://openalex.org/W2106596127","https://openalex.org/W2114703458","https://openalex.org/W2118587067","https://openalex.org/W2130494035","https://openalex.org/W2131456395","https://openalex.org/W2135000328","https://openalex.org/W2136422121","https://openalex.org/W2142070680","https://openalex.org/W2142635246","https://openalex.org/W2150926065","https://openalex.org/W2153562609","https://openalex.org/W2187417714","https://openalex.org/W4213387068","https://openalex.org/W4247420482"],"related_works":["https://openalex.org/W2804364458","https://openalex.org/W4298130764","https://openalex.org/W2132641928","https://openalex.org/W2086525401","https://openalex.org/W2090259340","https://openalex.org/W4310225030","https://openalex.org/W2083665254","https://openalex.org/W2393816671","https://openalex.org/W1534720161","https://openalex.org/W2804957450"],"abstract_inverted_index":{"BACKGROUND:":[0],"Recent":[1],"analyses":[2],"have":[3,25],"suggested":[4],"that":[5,14],"many":[6],"genes":[7],"possess":[8],"multiple":[9],"transcription":[10],"start":[11],"sites":[12],"(TSSs)":[13],"are":[15],"differentially":[16],"utilized":[17],"in":[18,61,134,170],"different":[19],"tissues":[20],"and":[21,69,75,88,132,162,176],"cell":[22],"lines.":[23],"We":[24,82,113],"identified":[26],"a":[27,70,84,99,146,150,156],"huge":[28,64],"number":[29],"of":[30,41,66,86,95,102,110,127,130,159],"TSSs":[31,96,121],"mapped":[32],"onto":[33],"the":[34,38,77,108,115,173],"mouse":[35],"genome":[36],"using":[37],"cap":[39],"analysis":[40],"gene":[42],"expression":[43,93,117,152],"(CAGE)":[44],"method.":[45],"The":[46,140],"standard":[47],"hierarchical":[48,87],"clustering":[49,90],"algorithm,":[50],"which":[51],"gives":[52],"us":[53],"easily":[54],"understandable":[55],"graphical":[56],"tree":[57],"images,":[58],"has":[59],"difficulties":[60],"processing":[62],"such":[63],"amounts":[65],"TSS":[67,164,184],"data":[68,104],"better":[71],"method":[72],"to":[73,91,105],"calculate":[74],"display":[76],"results":[78],"is":[79,177],"needed.":[80],"RESULTS:":[81],"use":[83],"combination":[85],"non-hierarchical":[89],"cluster":[92,147],"profiles":[94],"based":[97],"on":[98],"large":[100],"amount":[101],"CAGE":[103],"profit":[106],"from":[107,123],"best":[109],"both":[111],"methods.":[112],"processed":[114],"genome-wide":[116],"data,":[118],"including":[119],"159,075":[120],"derived":[122],"127":[124],"RNA":[125,161],"samples":[126],"various":[128],"organs":[129],"mouse,":[131],"succeeded":[133,169],"categorizing":[135],"them":[136],"into":[137],"70-100":[138],"clusters.":[139],"clusters":[141],"exhibited":[142],"intriguing":[143],"biological":[144],"features:":[145],"supergroup":[148],"with":[149],"ubiquitous":[151],"profile,":[153],"tissue-specific":[154],"patterns,":[155],"distinct":[157],"distribution":[158],"non-coding":[160],"functional":[163],"groups.":[165],"CONCLUSION:":[166],"Our":[167],"approach":[168],"greatly":[171],"reducing":[172],"calculation":[174],"cost,":[175],"an":[178],"appropriate":[179],"solution":[180],"for":[181],"analyzing":[182],"large-scale":[183],"usage":[185],"data.":[186]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}