{"id":"https://openalex.org/W4409121227","doi":"https://doi.org/10.1093/bioinformatics/btaf133","title":"AlertGS: determining alerts for gene sets","display_name":"AlertGS: determining alerts for gene sets","publication_year":2025,"publication_date":"2025-03-29","ids":{"openalex":"https://openalex.org/W4409121227","doi":"https://doi.org/10.1093/bioinformatics/btaf133","pmid":"https://pubmed.ncbi.nlm.nih.gov/40178932"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf133","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf133","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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/bioinformatics/btaf133","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059609442","display_name":"Franziska Kappenberg","orcid":"https://orcid.org/0000-0001-8066-5333"},"institutions":[{"id":"https://openalex.org/I200332995","display_name":"TU Dortmund University","ror":"https://ror.org/01k97gp34","country_code":"DE","type":"education","lineage":["https://openalex.org/I200332995"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Franziska Kappenberg","raw_affiliation_strings":["Department of Statistics, TU Dortmund University , 44227 Dortmund,","TU Dortmund University Department of Statistics, , Dortmund, 44227,"],"raw_orcid":"https://orcid.org/0000-0001-8066-5333","affiliations":[{"raw_affiliation_string":"Department of Statistics, TU Dortmund University , 44227 Dortmund,","institution_ids":["https://openalex.org/I200332995"]},{"raw_affiliation_string":"TU Dortmund University Department of Statistics, , Dortmund, 44227,","institution_ids":["https://openalex.org/I200332995"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075610512","display_name":"J\u00f6rg Rahnenf\u00fchrer","orcid":"https://orcid.org/0000-0002-8947-440X"},"institutions":[{"id":"https://openalex.org/I200332995","display_name":"TU Dortmund University","ror":"https://ror.org/01k97gp34","country_code":"DE","type":"education","lineage":["https://openalex.org/I200332995"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"J\u00f6rg Rahnenf\u00fchrer","raw_affiliation_strings":["Department of Statistics, TU Dortmund University , 44227 Dortmund,","TU Dortmund University Department of Statistics, , Dortmund, 44227,"],"raw_orcid":"https://orcid.org/0000-0002-8947-440X","affiliations":[{"raw_affiliation_string":"Department of Statistics, TU Dortmund University , 44227 Dortmund,","institution_ids":["https://openalex.org/I200332995"]},{"raw_affiliation_string":"TU Dortmund University Department of Statistics, , Dortmund, 44227,","institution_ids":["https://openalex.org/I200332995"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I200332995"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0511005,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9718000292778015,"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":0.9718000292778015,"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":0.004800000227987766,"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/T12867","display_name":"Advanced Biosensing Techniques and Applications","score":0.002300000051036477,"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":0.6922664642333984},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.6470842361450195},{"id":"https://openalex.org/keywords/decorrelation","display_name":"Decorrelation","score":0.6056621670722961},{"id":"https://openalex.org/keywords/statistic","display_name":"Statistic","score":0.5790635943412781},{"id":"https://openalex.org/keywords/statement","display_name":"Statement (logic)","score":0.5789452791213989},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5468527674674988},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.511982262134552},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.38566792011260986},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2506200075149536},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2176649272441864},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2173621654510498},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.2124972939491272},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.18351617455482483},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10773944854736328}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6922664642333984},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6470842361450195},{"id":"https://openalex.org/C177860922","wikidata":"https://www.wikidata.org/wiki/Q788608","display_name":"Decorrelation","level":2,"score":0.6056621670722961},{"id":"https://openalex.org/C89128539","wikidata":"https://www.wikidata.org/wiki/Q1949963","display_name":"Statistic","level":2,"score":0.5790635943412781},{"id":"https://openalex.org/C2777026412","wikidata":"https://www.wikidata.org/wiki/Q2684591","display_name":"Statement (logic)","level":2,"score":0.5789452791213989},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5468527674674988},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.511982262134552},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38566792011260986},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2506200075149536},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2176649272441864},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2173621654510498},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.2124972939491272},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.18351617455482483},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10773944854736328},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[{"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":"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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf133","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf133","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40178932","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40178932","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12041417","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12041417","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf133","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf133","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2493638443","display_name":"GRK 2624: Biostatistische Methoden f\u00fcr hochdimensionale Daten in der Toxikologie","funder_award_id":"427806116","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W2030371558","https://openalex.org/W2100980426","https://openalex.org/W2103017472","https://openalex.org/W2110065044","https://openalex.org/W2120024428","https://openalex.org/W2123106337","https://openalex.org/W2124562077","https://openalex.org/W2130410032","https://openalex.org/W2179438025","https://openalex.org/W2560627368","https://openalex.org/W2942877471","https://openalex.org/W2979832776","https://openalex.org/W3125922066","https://openalex.org/W3199019000","https://openalex.org/W4212974063","https://openalex.org/W4231254854","https://openalex.org/W4294216483","https://openalex.org/W4309247346","https://openalex.org/W4396749390","https://openalex.org/W6906534812"],"related_works":["https://openalex.org/W1604939135","https://openalex.org/W2127058578","https://openalex.org/W2098040275","https://openalex.org/W2735368845","https://openalex.org/W2089764958","https://openalex.org/W3109905219","https://openalex.org/W2073586885","https://openalex.org/W2546477360","https://openalex.org/W2359691516","https://openalex.org/W2261979314"],"abstract_inverted_index":{"MOTIVATION:":[0],"A":[1],"typical":[2],"goal":[3],"in":[4],"gene":[5,11,21,65,84,101,121,140],"expression":[6,22],"studies":[7],"is":[8,53,91,167],"identifying":[9],"certain":[10],"sets":[12,111,122],"enriched":[13],"with":[14,123],"significant":[15],"genes.":[16],"The":[17,89,126,155],"measurement":[18],"of":[19,33,44,59,82,109,119],"many":[20],"experiments":[23],"for":[24,37,99,116],"several":[25],"concentrations":[26],"or":[27,76],"time":[28,77],"points":[29],"allows":[30],"the":[31,34,41,57,73,79,83,138,160,164,170],"modeling":[32],"concentration/time-response":[35],"relationship":[36],"each":[38,100],"gene,":[39],"and":[40,72,146,162],"subsequent":[42,134],"estimation":[43],"a":[45,68,94,107,124],"gene-wise":[46],"alert.":[47],"In":[48],"this":[49],"work,":[50],"an":[51],"approach":[52],"proposed":[54],"to":[55,64,149,158],"transfer":[56],"concept":[58],"alerts":[60,142],"from":[61],"single":[62],"genes":[63],"sets,":[66],"yielding":[67],"global":[69],"significance":[70],"statement":[71],"respective":[74],"concentration":[75],"where":[78],"first":[80],"enrichment":[81],"set":[85],"can":[86,112,130],"be":[87,113,131,150],"observed.":[88],"methodology":[90,166],"based":[92],"on":[93],"Kolmogorov-Smirnoff":[95],"type":[96],"test":[97],"statistic":[98],"set.":[102],"RESULTS:":[103],"Simulations":[104],"show":[105],"that":[106],"majority":[108],"these":[110],"identified":[114],"especially":[115],"lower":[117],"numbers":[118],"true":[120,139],"signal.":[125],"false":[127],"positive":[128],"rate":[129],"controlled":[132],"by":[133],"decorrelation":[135],"approaches.":[136],"Overall,":[137],"set-wise":[141],"are":[143],"rarely":[144],"overestimated":[145],"rather":[147],"tend":[148],"underestimated.":[151],"AVAILABILITY":[152],"AND":[153],"IMPLEMENTATION:":[154],"code":[156],"needed":[157],"reproduce":[159],"simulations":[161],"apply":[163],"AlertGS":[165],"available":[168],"at":[169],"GitHub":[171],"repository:":[172],"https://github.com/FKappenberg/AlertGS.":[173]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
