{"id":"https://openalex.org/W2586834698","doi":"https://doi.org/10.1186/s13040-017-0125-9","title":"Gene set analysis controlling for length bias in RNA-seq experiments","display_name":"Gene set analysis controlling for length bias in RNA-seq experiments","publication_year":2017,"publication_date":"2017-02-06","ids":{"openalex":"https://openalex.org/W2586834698","doi":"https://doi.org/10.1186/s13040-017-0125-9","mag":"2586834698","pmid":"https://pubmed.ncbi.nlm.nih.gov/28184252"},"language":"en","primary_location":{"id":"doi:10.1186/s13040-017-0125-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-017-0125-9","pdf_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-017-0125-9","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-017-0125-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102761227","display_name":"Xing Ren","orcid":null},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xing Ren","raw_affiliation_strings":["Department of Biostatistics, SUNY University at Buffalo, Buffalo, 14214 USA","Department of Biostatistics, SUNY University at Buffalo, Buffalo, 14214, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, SUNY University at Buffalo, Buffalo, 14214 USA","institution_ids":["https://openalex.org/I63190737"]},{"raw_affiliation_string":"Department of Biostatistics, SUNY University at Buffalo, Buffalo, 14214, USA","institution_ids":["https://openalex.org/I63190737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056585446","display_name":"Qiang Hu","orcid":"https://orcid.org/0000-0002-4090-5539"},"institutions":[{"id":"https://openalex.org/I1292894508","display_name":"Roswell Park Comprehensive Cancer Center","ror":"https://ror.org/0499dwk57","country_code":"US","type":"facility","lineage":["https://openalex.org/I1292894508"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qiang Hu","raw_affiliation_strings":["Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, 14263 USA","Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, 14263, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, 14263 USA","institution_ids":["https://openalex.org/I1292894508"]},{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, 14263, USA","institution_ids":["https://openalex.org/I1292894508"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100339575","display_name":"Song Liu","orcid":"https://orcid.org/0000-0001-6351-2941"},"institutions":[{"id":"https://openalex.org/I1292894508","display_name":"Roswell Park Comprehensive Cancer Center","ror":"https://ror.org/0499dwk57","country_code":"US","type":"facility","lineage":["https://openalex.org/I1292894508"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Song Liu","raw_affiliation_strings":["Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, 14263 USA","Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, 14263, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, 14263 USA","institution_ids":["https://openalex.org/I1292894508"]},{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, 14263, USA","institution_ids":["https://openalex.org/I1292894508"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100373518","display_name":"Jianmin Wang","orcid":"https://orcid.org/0000-0001-7527-0409"},"institutions":[{"id":"https://openalex.org/I1292894508","display_name":"Roswell Park Comprehensive Cancer Center","ror":"https://ror.org/0499dwk57","country_code":"US","type":"facility","lineage":["https://openalex.org/I1292894508"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jianmin Wang","raw_affiliation_strings":["Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, 14263 USA","Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, 14263, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, 14263 USA","institution_ids":["https://openalex.org/I1292894508"]},{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, 14263, USA","institution_ids":["https://openalex.org/I1292894508"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018381838","display_name":"Jeffrey C. Miecznikowski","orcid":"https://orcid.org/0000-0003-0759-5118"},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeffrey C. Miecznikowski","raw_affiliation_strings":["Department of Biostatistics, SUNY University at Buffalo, Buffalo, 14214 USA","Department of Biostatistics, SUNY University at Buffalo, Buffalo, 14214, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, SUNY University at Buffalo, Buffalo, 14214 USA","institution_ids":["https://openalex.org/I63190737"]},{"raw_affiliation_string":"Department of Biostatistics, SUNY University at Buffalo, Buffalo, 14214, USA","institution_ids":["https://openalex.org/I63190737"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.5608,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.6533502,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"10","issue":"1","first_page":"5","last_page":"5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.6797000169754028,"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":0.6797000169754028,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.1485999971628189,"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":0.06769999861717224,"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":0.5724669694900513},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5653718709945679},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5639002919197083},{"id":"https://openalex.org/keywords/data-set","display_name":"Data set","score":0.42819932103157043},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4087521433830261},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35780635476112366},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3356442451477051},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.328378826379776},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2586575746536255},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22284990549087524},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.20393192768096924},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.16738659143447876},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.10615524649620056}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.5724669694900513},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5653718709945679},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5639002919197083},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.42819932103157043},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4087521433830261},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35780635476112366},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3356442451477051},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.328378826379776},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2586575746536255},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22284990549087524},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.20393192768096924},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.16738659143447876},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.10615524649620056},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/s13040-017-0125-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-017-0125-9","pdf_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-017-0125-9","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:28184252","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28184252","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":"BioData mining","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:5294840","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5294840","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Min","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13040-017-0125-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-017-0125-9","pdf_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-017-0125-9","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1220424006","display_name":null,"funder_award_id":"CA016056","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G8529445282","display_name":null,"funder_award_id":"P30 CA016056","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"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/W2586834698.pdf","grobid_xml":"https://content.openalex.org/works/W2586834698.grobid-xml"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W170656029","https://openalex.org/W1486681857","https://openalex.org/W1510659740","https://openalex.org/W1545338101","https://openalex.org/W1597029348","https://openalex.org/W1966799302","https://openalex.org/W1979217028","https://openalex.org/W1989367702","https://openalex.org/W1992953482","https://openalex.org/W2006355599","https://openalex.org/W2007302877","https://openalex.org/W2016474243","https://openalex.org/W2020859582","https://openalex.org/W2022590976","https://openalex.org/W2027043259","https://openalex.org/W2046233258","https://openalex.org/W2047993539","https://openalex.org/W2056099894","https://openalex.org/W2091975751","https://openalex.org/W2094229518","https://openalex.org/W2097065948","https://openalex.org/W2100980426","https://openalex.org/W2102074241","https://openalex.org/W2103017472","https://openalex.org/W2104976021","https://openalex.org/W2105022693","https://openalex.org/W2107018762","https://openalex.org/W2107060225","https://openalex.org/W2110065044","https://openalex.org/W2112220625","https://openalex.org/W2114104545","https://openalex.org/W2114504176","https://openalex.org/W2118069309","https://openalex.org/W2119034410","https://openalex.org/W2122863959","https://openalex.org/W2123106337","https://openalex.org/W2130410032","https://openalex.org/W2139036189","https://openalex.org/W2140954822","https://openalex.org/W2142165994","https://openalex.org/W2145825942","https://openalex.org/W2146436369","https://openalex.org/W2146512944","https://openalex.org/W2148167644","https://openalex.org/W2150414518","https://openalex.org/W2152239989","https://openalex.org/W2159707944","https://openalex.org/W2162148674","https://openalex.org/W2166550754","https://openalex.org/W2167119716","https://openalex.org/W2170219300","https://openalex.org/W2170551349","https://openalex.org/W3100378224","https://openalex.org/W4300577719","https://openalex.org/W6685184340"],"related_works":["https://openalex.org/W4234711916","https://openalex.org/W2027108423","https://openalex.org/W1855666948","https://openalex.org/W2758561209","https://openalex.org/W1548095260","https://openalex.org/W2343361478","https://openalex.org/W2594414941","https://openalex.org/W2781711915","https://openalex.org/W2112817590","https://openalex.org/W1555291398"],"abstract_inverted_index":{"BACKGROUND:":[0],"In":[1,71],"gene":[2,12,49,77,82,91,102,126,143,149,176,202,215,224,233],"set":[3,92,103,127,203],"analysis,":[4],"the":[5,11,27,56,63,67,74,115,125,138,141,148,160,171,182,192,229,237],"researchers":[6],"are":[7,15,179],"interested":[8],"in":[9,48,54,90,159],"determining":[10],"sets":[13,177,234],"that":[14,178,188],"significantly":[16],"correlated":[17,80],"with":[18,81,105,197,217],"an":[19,41],"outcome,":[20],"e.g.":[21],"disease":[22],"status":[23],"or":[24],"treatment.":[25],"With":[26],"rapid":[28],"development":[29],"of":[30,66,76,137,140,163,173],"high":[31],"throughput":[32],"sequencing":[33,37],"technologies,":[34],"Ribonucleic":[35],"acid":[36],"(RNA-seq)":[38],"has":[39],"become":[40],"important":[42],"alternative":[43],"to":[44,59,231],"traditional":[45],"expression":[46,50,78],"arrays":[47],"studies.":[51],"Challenges":[52],"exist":[53],"adopting":[55],"existent":[57],"algorithms":[58],"RNA-seq":[60,72,110,218],"data":[61,219],"given":[62],"intrinsic":[64],"difference":[65],"technologies":[68],"and":[69,239],"data.":[70,111],"experiments,":[73],"measure":[75],"is":[79,208],"length.":[83],"This":[84],"inherent":[85,223],"correlation":[86],"may":[87],"cause":[88],"bias":[89,107,238],"analysis.":[93],"RESULTS:":[94],"We":[95,166,185],"develop":[96],"SeqGSA,":[97],"a":[98,154,209],"new":[99],"method":[100,123,169,190,200],"for":[101,109,120,147,201,212,222],"analysis":[104],"length":[106,150,183,225],"adjustment":[108],"It":[112,227],"extends":[113],"from":[114],"R":[116],"package":[117],"GSA":[118],"designed":[119],"microarrays.":[121],"Our":[122],"compares":[124],"maxmean":[128],"statistic":[129],"against":[130],"permutations,":[131],"while":[132,220],"also":[133,186],"taking":[134],"into":[135],"account":[136],"statistics":[139],"other":[142],"sets.":[144],"To":[145],"adjust":[146],"bias,":[151],"we":[152],"implement":[153],"flexible":[155],"weighted":[156],"sampling":[157],"scheme":[158],"restandardization":[161],"step":[162],"our":[164,168,189],"algorithm.":[165],"show":[167,187],"improves":[170],"power":[172,230],"identifying":[174],"significant":[175,214],"affected":[180,235],"by":[181,236],"bias.":[184],"maintains":[191,240],"type":[193,241],"I":[194,242],"error":[195,243],"comparing":[196],"another":[198],"representative":[199],"enrichment":[204],"test.":[205],"CONCLUSIONS:":[206],"SeqGSA":[207],"promising":[210],"tool":[211],"testing":[213],"pathways":[216],"adjusting":[221],"effect.":[226],"enhances":[228],"detect":[232],"under":[244],"various":[245],"situations.":[246]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
