{"id":"https://openalex.org/W4292261953","doi":"https://doi.org/10.1186/s12859-022-04884-8","title":"SEMgsa: topology-based pathway enrichment analysis with structural equation models","display_name":"SEMgsa: topology-based pathway enrichment analysis with structural equation models","publication_year":2022,"publication_date":"2022-08-17","ids":{"openalex":"https://openalex.org/W4292261953","doi":"https://doi.org/10.1186/s12859-022-04884-8","pmid":"https://pubmed.ncbi.nlm.nih.gov/35978279"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-022-04884-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04884-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04884-8","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/s12859-022-04884-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052156750","display_name":"Mario Grassi","orcid":"https://orcid.org/0000-0001-6612-8566"},"institutions":[{"id":"https://openalex.org/I25217355","display_name":"University of Pavia","ror":"https://ror.org/00s6t1f81","country_code":"IT","type":"education","lineage":["https://openalex.org/I25217355"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Mario Grassi","raw_affiliation_strings":["Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy","institution_ids":["https://openalex.org/I25217355"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059863311","display_name":"Barbara Tarantino","orcid":"https://orcid.org/0000-0001-6384-2561"},"institutions":[{"id":"https://openalex.org/I25217355","display_name":"University of Pavia","ror":"https://ror.org/00s6t1f81","country_code":"IT","type":"education","lineage":["https://openalex.org/I25217355"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Barbara Tarantino","raw_affiliation_strings":["Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy. barbara.tarantino@unipv.it","Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy"],"raw_orcid":"https://orcid.org/0000-0001-6384-2561","affiliations":[{"raw_affiliation_string":"Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy. barbara.tarantino@unipv.it","institution_ids":["https://openalex.org/I25217355"]},{"raw_affiliation_string":"Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy","institution_ids":["https://openalex.org/I25217355"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5059863311"],"corresponding_institution_ids":["https://openalex.org/I25217355"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.3132,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.50866306,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"23","issue":"1","first_page":"344","last_page":"344"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9768999814987183,"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":0.9768999814987183,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.006500000134110451,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.002400000113993883,"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/computer-science","display_name":"Computer science","score":0.654568076133728},{"id":"https://openalex.org/keywords/network-topology","display_name":"Network topology","score":0.48995891213417053},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.48224955797195435},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.46309661865234375},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4545958340167999},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.43960991501808167},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4351623058319092},{"id":"https://openalex.org/keywords/structural-equation-modeling","display_name":"Structural equation modeling","score":0.41277146339416504},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3848715126514435},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3800783157348633},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2235071063041687},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21690988540649414}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.654568076133728},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.48995891213417053},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.48224955797195435},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.46309661865234375},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4545958340167999},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.43960991501808167},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4351623058319092},{"id":"https://openalex.org/C71104824","wikidata":"https://www.wikidata.org/wiki/Q1476639","display_name":"Structural equation modeling","level":2,"score":0.41277146339416504},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3848715126514435},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3800783157348633},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2235071063041687},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21690988540649414},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-022-04884-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04884-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04884-8","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:35978279","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35978279","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:pubmedcentral.nih.gov:9385099","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9385099","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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:0e1fd2218db947dd9cdfdff23c12b94a","is_oa":true,"landing_page_url":"https://doaj.org/article/0e1fd2218db947dd9cdfdff23c12b94a","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 23, Iss 1, Pp 1-20 (2022)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-022-04884-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04884-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04884-8","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":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.4699999988079071}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322874","display_name":"Universit\u00e0 degli Studi di Pavia","ror":"https://ror.org/00s6t1f81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4292261953.pdf","grobid_xml":"https://content.openalex.org/works/W4292261953.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W52354453","https://openalex.org/W52410658","https://openalex.org/W1848567445","https://openalex.org/W1966315727","https://openalex.org/W1979616603","https://openalex.org/W1982754045","https://openalex.org/W1983463159","https://openalex.org/W1989277387","https://openalex.org/W1990512452","https://openalex.org/W2000190151","https://openalex.org/W2009501477","https://openalex.org/W2020859582","https://openalex.org/W2054892633","https://openalex.org/W2084533385","https://openalex.org/W2100980426","https://openalex.org/W2109912704","https://openalex.org/W2110065044","https://openalex.org/W2110687686","https://openalex.org/W2119454933","https://openalex.org/W2122863959","https://openalex.org/W2129099812","https://openalex.org/W2130410032","https://openalex.org/W2134736660","https://openalex.org/W2154972152","https://openalex.org/W2157646380","https://openalex.org/W2159482845","https://openalex.org/W2263356566","https://openalex.org/W2330978860","https://openalex.org/W2332308455","https://openalex.org/W2763097300","https://openalex.org/W2963190765","https://openalex.org/W2984996233","https://openalex.org/W3035249419","https://openalex.org/W3170522992","https://openalex.org/W3176496038","https://openalex.org/W3207983471","https://openalex.org/W4231254854","https://openalex.org/W4293567165","https://openalex.org/W4294216483","https://openalex.org/W4298091299","https://openalex.org/W6813094581"],"related_works":["https://openalex.org/W2024934382","https://openalex.org/W2303173273","https://openalex.org/W2513767888","https://openalex.org/W3147308590","https://openalex.org/W1528049813","https://openalex.org/W1968285868","https://openalex.org/W2364043478","https://openalex.org/W4388140417","https://openalex.org/W3153451317","https://openalex.org/W4313635805"],"abstract_inverted_index":{"BACKGROUND:":[0],"Pathway":[1],"enrichment":[2,234],"analysis":[3],"is":[4,161,226,257],"extensively":[5],"used":[6,123,193],"in":[7,107,130,181,205,259],"high-throughput":[8],"experimental":[9,79],"studies":[10],"to":[11,46,58,71,125,164,194,237,252],"gain":[12],"insight":[13],"into":[14,89,243],"the":[15,31,34,51,56,73,90,98,165,169,201,260],"functional":[16],"roles":[17],"of":[18,21,33,92,109,203,207,222],"pre-defined":[19],"subsets":[20],"genes,":[22],"proteins":[23],"and":[24,152,179,199,247],"metabolites.":[25],"Methods":[26],"that":[27,40],"leverages":[28],"information":[29,246],"on":[30],"topology":[32],"underlying":[35],"pathways":[36,166],"outperform":[37],"simpler":[38],"methods":[39,204],"only":[41],"consider":[42],"pathway":[43,189,249],"membership,":[44],"leading":[45],"improved":[47],"performance.":[48],"Among":[49],"all":[50],"proposed":[52],"software":[53,186],"tools,":[54],"there's":[55],"need":[57],"combine":[59,97],"high":[60,182],"statistical":[61,214],"power":[62],"together":[63,140],"with":[64,141,156,235],"a":[65,77,85,131,142,227],"user-friendly":[66],"framework,":[67],"making":[68],"it":[69],"difficult":[70],"choose":[72],"best":[74,219],"method":[75,231],"for":[76,168,232],"particular":[78],"environment.":[80],"RESULTS:":[81],"We":[82,122],"propose":[83],"SEMgsa,":[84],"topology-based":[86],"algorithm":[87],"developed":[88],"framework":[91],"structural":[93],"equation":[94],"models.":[95],"SEMgsa":[96,124,160,225,256],"SEM":[99],"p":[100,174],"values":[101,175],"regarding":[102],"node-specific":[103],"group":[104],"effect":[105],"estimates":[106],"terms":[108,206],"activation":[110],"or":[111],"inhibition,":[112],"after":[113],"statistically":[114],"controlling":[115],"biological":[116,254],"relations":[117],"among":[118],"genes":[119],"within":[120],"pathways.":[121],"identify":[126],"biologically":[127],"relevant":[128],"results":[129,217],"Coronavirus":[132],"disease":[133],"(COVID-19)":[134],"RNA-seq":[135],"dataset":[136,148],"(GEO":[137,149],"accession:":[138,150],"GSE172114)":[139],"frontotemporal":[143],"dementia":[144],"(FTD)":[145],"DNA":[146],"methylation":[147],"GSE53740)":[151],"compared":[153],"its":[154],"performance":[155,202,221],"some":[157],"existing":[158,185],"methods.":[159],"highly":[162],"sensitive":[163],"designed":[167],"specific":[170],"disease,":[171],"showing":[172],"low":[173],"([Formula:":[176],"see":[177],"text])":[178],"ranking":[180],"positions,":[183],"outperforming":[184],"tools.":[187],"Three":[188],"dysregulation":[190],"mechanisms":[191],"were":[192],"generate":[195],"simulated":[196],"expression":[197,239],"data":[198],"evaluate":[200],"type":[208],"I":[209],"error":[210],"followed":[211],"by":[212],"their":[213],"power.":[215],"Simulation":[216],"confirm":[218],"overall":[220],"SEMgsa.":[223],"CONCLUSIONS:":[224],"novel":[228],"yet":[229],"powerful":[230],"identifying":[233],"regard":[236],"gene":[238],"data.":[240],"It":[241],"takes":[242],"account":[244],"topological":[245],"exploits":[248],"perturbation":[250],"statistics":[251],"reveal":[253],"information.":[255],"implemented":[258],"R":[261],"package":[262],"SEMgraph,":[263],"easily":[264],"available":[265],"at":[266],"https://CRAN.R-project.org/package=SEMgraph":[267],".":[268]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
