{"id":"https://openalex.org/W7134176020","doi":"https://doi.org/10.1093/bib/bbag061","title":"Finding Significant Hits in Networks: a network-based tool for analyzing gene-level <i>P</i> -values to identify significant genes missed by standard methods","display_name":"Finding Significant Hits in Networks: a network-based tool for analyzing gene-level <i>P</i> -values to identify significant genes missed by standard methods","publication_year":2026,"publication_date":"2026-01-28","ids":{"openalex":"https://openalex.org/W7134176020","doi":"https://doi.org/10.1093/bib/bbag061","pmid":"https://pubmed.ncbi.nlm.nih.gov/41795654"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbag061","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag061","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bib/bbag061","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5126553065","display_name":"Sandeep Acharya","orcid":null},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sandeep Acharya","raw_affiliation_strings":["Division of Computational and Data Sciences, Washington University , 1 Brookings Dr, St. Louis, MO 63130 ,"],"raw_orcid":"https://orcid.org/0000-0001-8046-0688","affiliations":[{"raw_affiliation_string":"Division of Computational and Data Sciences, Washington University , 1 Brookings Dr, St. Louis, MO 63130 ,","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090396769","display_name":"Vaha Akbary Moghaddam","orcid":"https://orcid.org/0000-0002-9910-0161"},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vaha Akbary Moghaddam","raw_affiliation_strings":["Division of Statistical Genomics, Washington University School of Medicine , 4515 McKinley Ave, St. Louis, MO 63110 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Statistical Genomics, Washington University School of Medicine , 4515 McKinley Ave, St. Louis, MO 63110 ,","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084806853","display_name":"Wooseok J. Jung","orcid":"https://orcid.org/0000-0001-8439-2133"},"institutions":[{"id":"https://openalex.org/I115283149","display_name":"Brookings Institution","ror":"https://ror.org/04aj4sh46","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I115283149"]},{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wooseok J Jung","raw_affiliation_strings":["Department of Computer Science and Engineering, Washington University , 1 Brookings Dr, St. Louis, MO 63130 ,"],"raw_orcid":"https://orcid.org/0000-0001-8439-2133","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Washington University , 1 Brookings Dr, St. Louis, MO 63130 ,","institution_ids":["https://openalex.org/I204465549","https://openalex.org/I115283149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048774782","display_name":"Yu Sung Kang","orcid":"https://orcid.org/0009-0009-4605-6353"},"institutions":[{"id":"https://openalex.org/I115283149","display_name":"Brookings Institution","ror":"https://ror.org/04aj4sh46","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I115283149"]},{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yu S Kang","raw_affiliation_strings":["Department of Computer Science and Engineering, Washington University , 1 Brookings Dr, St. Louis, MO 63130 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Washington University , 1 Brookings Dr, St. Louis, MO 63130 ,","institution_ids":["https://openalex.org/I204465549","https://openalex.org/I115283149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110609462","display_name":"Shu Liao","orcid":null},"institutions":[{"id":"https://openalex.org/I115283149","display_name":"Brookings Institution","ror":"https://ror.org/04aj4sh46","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I115283149"]},{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shu Liao","raw_affiliation_strings":["Department of Computer Science and Engineering, Washington University , 1 Brookings Dr, St. Louis, MO 63130 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Washington University , 1 Brookings Dr, St. Louis, MO 63130 ,","institution_ids":["https://openalex.org/I204465549","https://openalex.org/I115283149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112103186","display_name":"M. A. Province","orcid":null},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael A Province","raw_affiliation_strings":["Division of Statistical Genomics, Washington University School of Medicine , 4515 McKinley Ave, St. Louis, MO 63110 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Statistical Genomics, Washington University School of Medicine , 4515 McKinley Ave, St. Louis, MO 63110 ,","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010345611","display_name":"Michael R. Brent","orcid":"https://orcid.org/0000-0002-8689-0299"},"institutions":[{"id":"https://openalex.org/I115283149","display_name":"Brookings Institution","ror":"https://ror.org/04aj4sh46","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I115283149"]},{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael R Brent","raw_affiliation_strings":["Department of Computer Science and Engineering, Washington University , 1 Brookings Dr, St. Louis, MO 63130 ,"],"raw_orcid":"https://orcid.org/0000-0002-8689-0299","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Washington University , 1 Brookings Dr, St. Louis, MO 63130 ,","institution_ids":["https://openalex.org/I204465549","https://openalex.org/I115283149"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5126553065"],"corresponding_institution_ids":["https://openalex.org/I204465549"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.47088908,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.7876999974250793,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.7876999974250793,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.10090000182390213,"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/T14393","display_name":"Health, Environment, Cognitive Aging","score":0.010200000368058681,"subfield":{"id":"https://openalex.org/subfields/2307","display_name":"Health, Toxicology and Mutagenesis"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6484000086784363},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5619999766349792},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.5568000078201294},{"id":"https://openalex.org/keywords/association","display_name":"Association (psychology)","score":0.5407999753952026},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.525600016117096},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.41659998893737793}],"concepts":[{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6484000086784363},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5619999766349792},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.5568000078201294},{"id":"https://openalex.org/C142853389","wikidata":"https://www.wikidata.org/wiki/Q744778","display_name":"Association (psychology)","level":2,"score":0.5407999753952026},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.525600016117096},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4700999855995178},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.41659998893737793},{"id":"https://openalex.org/C12590798","wikidata":"https://www.wikidata.org/wiki/Q3933199","display_name":"Replication (statistics)","level":2,"score":0.40549999475479126},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.37940001487731934},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.36070001125335693},{"id":"https://openalex.org/C186413461","wikidata":"https://www.wikidata.org/wiki/Q744727","display_name":"Genetic association","level":5,"score":0.35830000042915344},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.33239999413490295},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3319999873638153},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.33009999990463257},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3249000012874603},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.289900004863739},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.26969999074935913},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.2655999958515167}],"mesh":[{"descriptor_ui":"D002318","descriptor_name":"Cardiovascular Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002318","descriptor_name":"Cardiovascular Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002318","descriptor_name":"Cardiovascular Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbag061","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag061","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41795654","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41795654","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:digitalcommons.wustl.edu:oa_4-7439","is_oa":true,"landing_page_url":"https://digitalcommons.wustl.edu/oa_4/6453","pdf_url":null,"source":{"id":"https://openalex.org/S4306400764","display_name":"Digital Commons@Becker (Washington University School of Medicine)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I204465549","host_organization_name":"Washington University in St. Louis","host_organization_lineage":["https://openalex.org/I204465549"],"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":"2020-Current year OA Pubs","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12967332","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12967332/","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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbag061","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag061","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G278200998","display_name":null,"funder_award_id":"HHSN268201500001I","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G4976486911","display_name":null,"funder_award_id":"75N92019D00031","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G5488772279","display_name":null,"funder_award_id":"N01-HC-25195","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"}],"funders":[{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":62,"referenced_works":["https://openalex.org/W1542816299","https://openalex.org/W1997407159","https://openalex.org/W2001554877","https://openalex.org/W2005970630","https://openalex.org/W2020541351","https://openalex.org/W2036747551","https://openalex.org/W2048048890","https://openalex.org/W2076513103","https://openalex.org/W2077157308","https://openalex.org/W2087212637","https://openalex.org/W2096173332","https://openalex.org/W2099800366","https://openalex.org/W2100869640","https://openalex.org/W2116759194","https://openalex.org/W2117242020","https://openalex.org/W2118258530","https://openalex.org/W2122713183","https://openalex.org/W2123170297","https://openalex.org/W2130410032","https://openalex.org/W2132145985","https://openalex.org/W2145025818","https://openalex.org/W2158057499","https://openalex.org/W2163953557","https://openalex.org/W2170146596","https://openalex.org/W2211287272","https://openalex.org/W2254879037","https://openalex.org/W2295275561","https://openalex.org/W2338895517","https://openalex.org/W2461482933","https://openalex.org/W2514905230","https://openalex.org/W2557530941","https://openalex.org/W2558534012","https://openalex.org/W2580897959","https://openalex.org/W2606498025","https://openalex.org/W2611696724","https://openalex.org/W2790280442","https://openalex.org/W2802891357","https://openalex.org/W2893701755","https://openalex.org/W2900668971","https://openalex.org/W2951144147","https://openalex.org/W2951144892","https://openalex.org/W2951538786","https://openalex.org/W2970771711","https://openalex.org/W2971586943","https://openalex.org/W2983166786","https://openalex.org/W2998273432","https://openalex.org/W3080999617","https://openalex.org/W3083058976","https://openalex.org/W3118594101","https://openalex.org/W3210119926","https://openalex.org/W4252021281","https://openalex.org/W4306353172","https://openalex.org/W4308616307","https://openalex.org/W4317866069","https://openalex.org/W4323036511","https://openalex.org/W4384346900","https://openalex.org/W4388978588","https://openalex.org/W4391724168","https://openalex.org/W4399127270","https://openalex.org/W4400098094","https://openalex.org/W4402538379","https://openalex.org/W4404443250"],"related_works":[],"abstract_inverted_index":{"Finding":[0],"Significant":[1],"Hits":[2],"in":[3,84,145],"Networks":[4],"(FISHNET)":[5],"uses":[6],"prior":[7],"biological":[8],"knowledge,":[9],"represented":[10],"as":[11],"gene":[12,16],"interaction":[13],"networks":[14,74],"and":[15,75,88,98,106,170,197],"function":[17,107],"annotations,":[18],"to":[19,95,101,113,127,226],"identify":[20,114],"genes":[21,62,78,120,154,158],"that":[22,61,82,121,137,156,172,178,199,205],"do":[23],"not":[24],"meet":[25],"the":[26,59,214],"genome-wide":[27,45,139,220],"significance":[28,140,221],"threshold":[29],"but":[30],"replicate,":[31],"nonetheless.":[32],"Its":[33],"input":[34],"is":[35,56,173,200,236],"gene-level":[36],"P-values":[37,64,81],"from":[38],"any":[39],"source,":[40],"including":[41],"omicsWAS,":[42],"aggregation":[43],"of":[44,118,152,157,213],"association":[46,166,193],"studies":[47],"P-values,":[48],"CRISPR":[49],"screens,":[50],"or":[51],"differential":[52],"expression":[53,169,196,208],"analysis.":[54],"It":[55],"based":[57],"on":[58],"idea":[60],"whose":[63],"are":[65,70,92],"low":[66],"purely":[67],"by":[68,175,202,231],"chance":[69,97],"distributed":[71],"randomly":[72],"across":[73],"functions,":[76],"so":[77],"with":[79,109,159],"suggestive":[80],"cluster":[83],"densely":[85],"connected":[86],"subnetworks":[87],"share":[89],"common":[90],"functions":[91],"less":[93],"likely":[94,100],"reflect":[96],"more":[99],"replicate.":[102],"FISHNET":[103,124,132,153,162,189,234],"combines":[104],"network":[105],"analysis":[108],"permutation-based":[110],"P-value":[111],"thresholds":[112,141],"a":[115,164],"small":[116],"set":[117],"exceptional":[119],"we":[122],"call":[123],"genes.":[125],"Applied":[126],"11":[128],"cardiovascular":[129],"risk":[130],"traits,":[131],"identified":[133,163,191],"19":[134],"gene-trait":[135],"relationships":[136,229],"missed":[138,230],"but,":[142],"nonetheless,":[143],"replicated":[144],"an":[146,192],"independent":[147],"cohort.":[148],"The":[149],"replication":[150],"rate":[151],"matched":[155],"lower":[160],"P-values.":[161],"novel":[165],"between":[167,194],"RUNX1":[168,179],"HDL":[171,186],"supported":[174,201],"experimental":[176,203],"evidence":[177,204],"promotes":[180],"white":[181],"fat":[182],"browning,":[183],"which":[184],"increases":[185,209],"cholesterol":[187],"levels.":[188],"also":[190],"LTB":[195,207],"BMI":[198,210],"higher":[206],"via":[211],"activation":[212],"LT\u03b2R":[215],"pathway.":[216],"Both":[217],"associations":[218],"failed":[219],"thresholds,":[222],"highlighting":[223],"FISHNET's":[224],"ability":[225],"uncover":[227],"meaningful":[228],"traditional":[232],"methods.":[233],"software":[235],"freely":[237],"available":[238],"at":[239],"https://brentlab.github.io/fishnet/.":[240]},"counts_by_year":[],"updated_date":"2026-05-05T08:41:31.759640","created_date":"2026-03-09T00:00:00"}