{"id":"https://openalex.org/W2332308455","doi":"https://doi.org/10.1109/jproc.2016.2531000","title":"A Novel Pathway Analysis Approach Based on the Unexplained Disregulation of Genes","display_name":"A Novel Pathway Analysis Approach Based on the Unexplained Disregulation of Genes","publication_year":2016,"publication_date":"2016-01-01","ids":{"openalex":"https://openalex.org/W2332308455","doi":"https://doi.org/10.1109/jproc.2016.2531000","mag":"2332308455","pmid":"https://pubmed.ncbi.nlm.nih.gov/30337764"},"language":"en","primary_location":{"id":"doi:10.1109/jproc.2016.2531000","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jproc.2016.2531000","pdf_url":null,"source":{"id":"https://openalex.org/S68686220","display_name":"Proceedings of the IEEE","issn_l":"0018-9219","issn":["0018-9219","1558-2256"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the IEEE","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6190577","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078307926","display_name":"Sahar Ansari","orcid":"https://orcid.org/0000-0001-7965-0927"},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sahar Ansari","raw_affiliation_strings":["Department of Computer Science, Wayne State University, Detroit, MI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Wayne State University, Detroit, MI, USA","institution_ids":["https://openalex.org/I185443292"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001054866","display_name":"C\u0103lin Voichi\u0163a","orcid":null},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Calin Voichita","raw_affiliation_strings":["Department of Computer Science, Wayne State University, Detroit, MI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Wayne State University, Detroit, MI, USA","institution_ids":["https://openalex.org/I185443292"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033124739","display_name":"Michele Donato","orcid":"https://orcid.org/0000-0002-9968-6027"},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michele Donato","raw_affiliation_strings":["Department of Computer Science, Wayne State University, Detroit, MI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Wayne State University, Detroit, MI, USA","institution_ids":["https://openalex.org/I185443292"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010830108","display_name":"Rebecca Tagett","orcid":"https://orcid.org/0000-0001-8604-7683"},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rebecca Tagett","raw_affiliation_strings":["Department of Computer Science, Wayne State University, Detroit, MI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Wayne State University, Detroit, MI, USA","institution_ids":["https://openalex.org/I185443292"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006190733","display_name":"Sorin Dr\u0103ghici","orcid":"https://orcid.org/0000-0002-0786-8377"},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sorin Draghici","raw_affiliation_strings":["Department of Computer Science, Wayne State University, Detroit, MI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Wayne State University, Detroit, MI, USA","institution_ids":["https://openalex.org/I185443292"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.8706,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.7600464,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"105","issue":"3","first_page":"1","last_page":"14"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.8859000205993652,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.8859000205993652,"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":0.021400000900030136,"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/T10949","display_name":"Genetic Neurodegenerative Diseases","score":0.016599999740719795,"subfield":{"id":"https://openalex.org/subfields/2804","display_name":"Cellular and Molecular Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/bioconductor","display_name":"Bioconductor","score":0.9812596440315247},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.7925257682800293},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6605614423751831},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.5825921297073364},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5537487268447876},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5499899387359619},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5489105582237244},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4609734117984772},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.45798149704933167},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4229498505592346},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3631019592285156},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33166640996932983},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.1227603554725647}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.9812596440315247},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.7925257682800293},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6605614423751831},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.5825921297073364},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5537487268447876},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5499899387359619},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5489105582237244},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4609734117984772},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.45798149704933167},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4229498505592346},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3631019592285156},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33166640996932983},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.1227603554725647},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1109/jproc.2016.2531000","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jproc.2016.2531000","pdf_url":null,"source":{"id":"https://openalex.org/S68686220","display_name":"Proceedings of the IEEE","issn_l":"0018-9219","issn":["0018-9219","1558-2256"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the IEEE","raw_type":"journal-article"},{"id":"pmid:30337764","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30337764","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":"Proceedings of the IEEE. Institute of Electrical and Electronics Engineers","raw_type":null},{"id":"pmh:oai:europepmc.org:5135558","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6190577","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6190577","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6190577","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proc IEEE Inst Electr Electron Eng","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:6190577","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6190577","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proc IEEE Inst Electr Electron Eng","raw_type":"Text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":59,"referenced_works":["https://openalex.org/W26839371","https://openalex.org/W101456243","https://openalex.org/W1417555467","https://openalex.org/W1440045881","https://openalex.org/W1546952499","https://openalex.org/W1606236576","https://openalex.org/W1972755526","https://openalex.org/W1977956545","https://openalex.org/W1978723648","https://openalex.org/W1983166842","https://openalex.org/W1984989438","https://openalex.org/W1986501321","https://openalex.org/W1989723191","https://openalex.org/W1993573917","https://openalex.org/W1994267372","https://openalex.org/W1996667997","https://openalex.org/W2001963295","https://openalex.org/W2007012192","https://openalex.org/W2016352369","https://openalex.org/W2018340043","https://openalex.org/W2020859582","https://openalex.org/W2030720530","https://openalex.org/W2034613288","https://openalex.org/W2038122249","https://openalex.org/W2042213574","https://openalex.org/W2044545697","https://openalex.org/W2050245934","https://openalex.org/W2058125715","https://openalex.org/W2061387301","https://openalex.org/W2068590125","https://openalex.org/W2070754102","https://openalex.org/W2080946103","https://openalex.org/W2086367553","https://openalex.org/W2089390825","https://openalex.org/W2091712128","https://openalex.org/W2100025044","https://openalex.org/W2100980426","https://openalex.org/W2105128106","https://openalex.org/W2106537627","https://openalex.org/W2109912704","https://openalex.org/W2110687686","https://openalex.org/W2112811019","https://openalex.org/W2114729479","https://openalex.org/W2121619336","https://openalex.org/W2129078779","https://openalex.org/W2129099812","https://openalex.org/W2130410032","https://openalex.org/W2135056923","https://openalex.org/W2135230352","https://openalex.org/W2136159134","https://openalex.org/W2138289111","https://openalex.org/W2143950810","https://openalex.org/W2146026944","https://openalex.org/W2147714160","https://openalex.org/W2154972152","https://openalex.org/W2158240093","https://openalex.org/W2159482845","https://openalex.org/W2582743722","https://openalex.org/W6628368890"],"related_works":["https://openalex.org/W2135678793","https://openalex.org/W2011682793","https://openalex.org/W2109288169","https://openalex.org/W2157684052","https://openalex.org/W2978247079","https://openalex.org/W2140163842","https://openalex.org/W2148708580","https://openalex.org/W3037604406","https://openalex.org/W2166887457","https://openalex.org/W3163106361"],"abstract_inverted_index":{"A":[0],"crucial":[1,142],"step":[2,117],"in":[3,21,39,101,144,224,228],"the":[4,10,14,51,54,61,70,95,102,108,125,145,161,168,172,202,211],"understanding":[5],"of":[6,13,64,72,91,98,110,124,164,171],"any":[7],"phenotype":[8],"is":[9,105,222],"correct":[11],"identification":[12],"signaling":[15,73],"pathways":[16,159],"that":[17,22,44,53,118,131,140,155,201],"are":[18,48],"significantly":[19,157],"impacted":[20,158],"phenotype.":[23,146],"However,":[24],"most":[25],"current":[26],"pathway":[27,152],"analysis":[28,153,221],"methods":[29,56],"produce":[30],"both":[31],"false":[32,37],"positives":[33],"as":[34,36,191,193],"well":[35,192],"negatives":[38],"certain":[40],"circumstances.":[41],"We":[42,128,147],"hypothesized":[43,130],"such":[45,132],"incorrect":[46],"results":[47,179],"due":[49],"to":[50,58,93,210],"fact":[52],"existing":[55],"fail":[57],"distinguish":[59],"between":[60],"primary":[62],"dis-regulation":[63,220],"a":[65,78,84,88,111,133,149],"given":[66],"gene":[67],"itself":[68],"and":[69,216,226],"effects":[71],"coming":[74],"from":[75],"upstream.":[76],"Furthermore,":[77],"modern":[79],"whole-genome":[80],"experiment":[81],"performed":[82],"with":[83,208],"next-generation":[85],"technology":[86],"spends":[87],"great":[89],"deal":[90],"effort":[92],"measure":[94],"entire":[96,162],"set":[97,163],"30,000-100,000":[99],"transcripts":[100],"genome.":[103],"This":[104],"followed":[106],"by":[107,175],"selection":[109],"few":[112],"hundreds":[113],"differentially":[114],"expressed":[115],"genes,":[116],"literally":[119],"discards":[120],"more":[121],"than":[122],"99%":[123],"collected":[126],"data.":[127],"also":[129],"drastic":[134],"filtering":[135],"could":[136],"discard":[137],"many":[138],"genes":[139],"play":[141],"roles":[143],"propose":[148],"novel":[150],"topology-based":[151],"method":[154,204],"identifies":[156],"using":[160],"measurements,":[165],"thus":[166],"allowing":[167],"full":[169],"use":[170],"data":[173,184,198],"provided":[174],"NGS":[176],"techniques.":[177],"The":[178],"obtained":[180],"on":[181,194],"24":[182],"real":[183],"sets":[185,199],"involving":[186],"12":[187],"different":[188],"human":[189],"diseases,":[190],"8":[195],"yeast":[196],"knock-out":[197],"show":[200],"proposed":[203],"yields":[205],"significant":[206],"improvements":[207],"respect":[209],"state-of-the-art":[212],"methods:":[213],"SPIA,":[214],"GSEA":[215],"GSA.":[217],"AVAILABILITY:":[218],"Primary":[219],"implemented":[223],"R":[225],"included":[227],"ROntoTools":[229],"Bioconductor":[230],"package":[231],"(versions":[232],"\u2265":[233],"2.0.0).":[234],"https://www.bioconductor.org/packages/release/bioc/html/ROntoTools.html.":[235]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}