{"id":"https://openalex.org/W2771315552","doi":"https://doi.org/10.1504/ijdmb.2017.10009477","title":"Analysis of clustered RNA-seq data","display_name":"Analysis of clustered RNA-seq data","publication_year":2017,"publication_date":"2017-01-01","ids":{"openalex":"https://openalex.org/W2771315552","doi":"https://doi.org/10.1504/ijdmb.2017.10009477","mag":"2771315552"},"language":"en","primary_location":{"id":"doi:10.1504/ijdmb.2017.10009477","is_oa":false,"landing_page_url":"https://doi.org/10.1504/ijdmb.2017.10009477","pdf_url":null,"source":{"id":"https://openalex.org/S35771696","display_name":"International Journal of Data Mining and Bioinformatics","issn_l":"1748-5673","issn":["1748-5673","1748-5681"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310317825","host_organization_name":"Inderscience Publishers","host_organization_lineage":["https://openalex.org/P4310317825"],"host_organization_lineage_names":["Inderscience Publishers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Data Mining and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100643662","display_name":"Taesung Park","orcid":"https://orcid.org/0000-0002-8294-590X"},"institutions":[{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Taesung Park","raw_affiliation_strings":["Department of Statistics, Seoul National University, South Korea"],"affiliations":[{"raw_affiliation_string":"Department of Statistics, Seoul National University, South Korea","institution_ids":["https://openalex.org/I139264467"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101881868","display_name":"Ye Jin Kim","orcid":"https://orcid.org/0000-0002-9743-8513"},"institutions":[{"id":"https://openalex.org/I31419693","display_name":"Kyungpook National University","ror":"https://ror.org/040c17130","country_code":"KR","type":"education","lineage":["https://openalex.org/I31419693"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Ye Jin Kim","raw_affiliation_strings":["Department of Food Science and Nutrition, Kyungpook National University, South Korea"],"affiliations":[{"raw_affiliation_string":"Department of Food Science and Nutrition, Kyungpook National University, South Korea","institution_ids":["https://openalex.org/I31419693"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109168263","display_name":"Myung Sook Choi","orcid":null},"institutions":[{"id":"https://openalex.org/I31419693","display_name":"Kyungpook National University","ror":"https://ror.org/040c17130","country_code":"KR","type":"education","lineage":["https://openalex.org/I31419693"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Myung Sook Choi","raw_affiliation_strings":["Department of Food Science and Nutrition, Kyungpook National University, South Korea"],"affiliations":[{"raw_affiliation_string":"Department of Food Science and Nutrition, Kyungpook National University, South Korea","institution_ids":["https://openalex.org/I31419693"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034909134","display_name":"Seungyeoun Lee","orcid":"https://orcid.org/0000-0001-7941-8933"},"institutions":[{"id":"https://openalex.org/I28777354","display_name":"Sejong University","ror":"https://ror.org/00aft1q37","country_code":"KR","type":"education","lineage":["https://openalex.org/I28777354"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Seungyeoun Lee","raw_affiliation_strings":["Department of Mathematics and Statistics, Sejong University, South Korea"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics, Sejong University, South Korea","institution_ids":["https://openalex.org/I28777354"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100328513","display_name":"Hyunjin Park","orcid":"https://orcid.org/0000-0001-5681-8918"},"institutions":[{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Hyunjin Park","raw_affiliation_strings":["Department of Statistics, Seoul National University, South Korea"],"affiliations":[{"raw_affiliation_string":"Department of Statistics, Seoul National University, South Korea","institution_ids":["https://openalex.org/I139264467"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5100643662"],"corresponding_institution_ids":["https://openalex.org/I139264467"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.14020051,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"19","issue":"1","first_page":"19","last_page":"19"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9842000007629395,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9842000007629395,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9835000038146973,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9763000011444092,"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/rna-seq","display_name":"RNA-Seq","score":0.6749055981636047},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5219166278839111},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5035139918327332},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4448951780796051},{"id":"https://openalex.org/keywords/gee","display_name":"Gee","score":0.41770240664482117},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3897654116153717},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3332363963127136},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3209919333457947},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.30703145265579224},{"id":"https://openalex.org/keywords/generalized-estimating-equation","display_name":"Generalized estimating equation","score":0.285791277885437},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17419177293777466},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.13874810934066772},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.134872168302536}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.6749055981636047},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5219166278839111},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5035139918327332},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4448951780796051},{"id":"https://openalex.org/C53084192","wikidata":"https://www.wikidata.org/wiki/Q1485121","display_name":"Gee","level":3,"score":0.41770240664482117},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3897654116153717},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3332363963127136},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3209919333457947},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.30703145265579224},{"id":"https://openalex.org/C27403532","wikidata":"https://www.wikidata.org/wiki/Q5532474","display_name":"Generalized estimating equation","level":2,"score":0.285791277885437},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17419177293777466},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.13874810934066772},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.134872168302536}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1504/ijdmb.2017.10009477","is_oa":false,"landing_page_url":"https://doi.org/10.1504/ijdmb.2017.10009477","pdf_url":null,"source":{"id":"https://openalex.org/S35771696","display_name":"International Journal of Data Mining and Bioinformatics","issn_l":"1748-5673","issn":["1748-5673","1748-5681"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310317825","host_organization_name":"Inderscience Publishers","host_organization_lineage":["https://openalex.org/P4310317825"],"host_organization_lineage_names":["Inderscience Publishers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Data Mining and Bioinformatics","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4382706259","https://openalex.org/W3216953802","https://openalex.org/W2315880189","https://openalex.org/W2588341283","https://openalex.org/W2408764787","https://openalex.org/W1980133991","https://openalex.org/W4385122440","https://openalex.org/W2808195958","https://openalex.org/W4312280763","https://openalex.org/W3002447856"],"abstract_inverted_index":{"RNA":[0],"sequencing":[1],"(RNA-seq)":[2],"technology":[3],"has":[4],"now":[5],"become":[6],"a":[7,96],"powerful":[8],"tool":[9],"for":[10],"measuring":[11],"levels":[12],"of":[13,51,146,152],"transcripts.":[14],"Through":[15,135],"this":[16,92],"high-throughput":[17],"technology,":[18],"we":[19,94,142],"can":[20],"investigate":[21],"post-transcriptional":[22],"modifications,":[23],"non-coding":[24],"RNAs,":[25],"mutations,":[26],"gene":[27,32],"fusion,":[28],"and":[29,139,174],"changes":[30],"in":[31,129,132],"expression":[33],"levels.":[34],"Recently,":[35],"many":[36],"methods":[37,53,84],"have":[38],"been":[39],"developed":[40],"to":[41,112,150,162,169,171],"find":[42],"differentially":[43],"expressed":[44],"genes":[45],"(DEGs)":[46],"between":[47,123],"treatment":[48],"groups.":[49],"Most":[50],"these":[52],"assume":[54],"that":[55],"RNA-seq":[56,67,76,89,124],"data":[57,68,125,137],"is":[58,109],"generated":[59],"independently":[60],"from":[61,78],"the":[62,79,102,121,144,147],"different":[63],"subjects.":[64],"Nowadays,":[65],"clustered":[66,88],"are":[69],"also":[70],"commonly":[71],"observed,":[72],"such":[73],"as":[74],"paired":[75],"data,":[77],"same":[80],"patient.":[81],"Unfortunately,":[82],"existing":[83,154],"cannot":[85],"adequately":[86],"handle":[87],"data.":[90,116],"In":[91],"paper,":[93],"propose":[95],"new":[97],"testing":[98],"method,":[99],"based":[100],"on":[101],"Generalised":[103],"Estimating":[104],"Equations":[105],"(GEE)":[106],"approach,":[107],"which":[108,127],"widely":[110],"used":[111],"analyse":[113],"repeatedly":[114],"measured":[115],"Our":[117],"GEE-based":[118],"approach":[119],"uses":[120],"correlations":[122],"appropriately,":[126],"results":[128],"increased":[130],"power":[131],"detecting":[133],"DEGs.":[134],"real":[136],"analysis":[138,159],"simulation":[140],"studies,":[141],"compare":[143],"performance":[145],"GEE":[148,158],"method":[149],"those":[151],"other":[153,164],"methods.":[155],"Specifically,":[156],"our":[157],"was":[160],"compared":[161],"various":[163],"methodologies,":[165],"particularly":[166],"with":[167],"regard":[168],"sensitivity":[170],"detect":[172],"DEGs":[173],"false":[175],"discovery":[176],"rates.":[177]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}