{"id":"https://openalex.org/W4377941318","doi":"https://doi.org/10.1093/bioinformatics/btad341","title":"KNeMAP: a network mapping approach for knowledge-driven comparison of transcriptomic profiles","display_name":"KNeMAP: a network mapping approach for knowledge-driven comparison of transcriptomic profiles","publication_year":2023,"publication_date":"2023-05-24","ids":{"openalex":"https://openalex.org/W4377941318","doi":"https://doi.org/10.1093/bioinformatics/btad341","pmid":"https://pubmed.ncbi.nlm.nih.gov/37225400"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad341","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad341","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad341/50439486/btad341.pdf","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://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad341/50439486/btad341.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032173283","display_name":"Alisa Pavel","orcid":"https://orcid.org/0000-0002-2983-0214"},"institutions":[{"id":"https://openalex.org/I166825849","display_name":"Tampere University","ror":"https://ror.org/033003e23","country_code":"FI","type":"education","lineage":["https://openalex.org/I166825849"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Alisa Pavel","raw_affiliation_strings":["BioMediTech Institute, Tampere University , 33520 Tampere, Finland","Faculty of Medicine and Health Technology, Tampere University , 33520 Tampere, Finland","Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE) , 33520 Tampere, Finland"],"raw_orcid":"https://orcid.org/0000-0002-2983-0214","affiliations":[{"raw_affiliation_string":"BioMediTech Institute, Tampere University , 33520 Tampere, Finland","institution_ids":["https://openalex.org/I166825849"]},{"raw_affiliation_string":"Faculty of Medicine and Health Technology, Tampere University , 33520 Tampere, Finland","institution_ids":["https://openalex.org/I166825849"]},{"raw_affiliation_string":"Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE) , 33520 Tampere, Finland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054987771","display_name":"Giusy del Giudice","orcid":"https://orcid.org/0000-0003-0999-4796"},"institutions":[{"id":"https://openalex.org/I166825849","display_name":"Tampere University","ror":"https://ror.org/033003e23","country_code":"FI","type":"education","lineage":["https://openalex.org/I166825849"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Giusy del Giudice","raw_affiliation_strings":["BioMediTech Institute, Tampere University , 33520 Tampere, Finland","Faculty of Medicine and Health Technology, Tampere University , 33520 Tampere, Finland","Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE) , 33520 Tampere, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioMediTech Institute, Tampere University , 33520 Tampere, Finland","institution_ids":["https://openalex.org/I166825849"]},{"raw_affiliation_string":"Faculty of Medicine and Health Technology, Tampere University , 33520 Tampere, Finland","institution_ids":["https://openalex.org/I166825849"]},{"raw_affiliation_string":"Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE) , 33520 Tampere, Finland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025810407","display_name":"Michele Fratello","orcid":"https://orcid.org/0000-0002-3997-2339"},"institutions":[{"id":"https://openalex.org/I166825849","display_name":"Tampere University","ror":"https://ror.org/033003e23","country_code":"FI","type":"education","lineage":["https://openalex.org/I166825849"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Michele Fratello","raw_affiliation_strings":["BioMediTech Institute, Tampere University , 33520 Tampere, Finland","Faculty of Medicine and Health Technology, Tampere University , 33520 Tampere, Finland","Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE) , 33520 Tampere, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioMediTech Institute, Tampere University , 33520 Tampere, Finland","institution_ids":["https://openalex.org/I166825849"]},{"raw_affiliation_string":"Faculty of Medicine and Health Technology, Tampere University , 33520 Tampere, Finland","institution_ids":["https://openalex.org/I166825849"]},{"raw_affiliation_string":"Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE) , 33520 Tampere, Finland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069490377","display_name":"L\u00e9o Ghemtio","orcid":"https://orcid.org/0000-0003-3591-5676"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Leo Ghemtio","raw_affiliation_strings":["Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki , 00790 Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki , 00790 Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045897474","display_name":"A. Di Lieto","orcid":"https://orcid.org/0000-0002-0265-7554"},"institutions":[{"id":"https://openalex.org/I4210106610","display_name":"National University Hospital of Iceland","ror":"https://ror.org/011k7k191","country_code":"IS","type":"funder","lineage":["https://openalex.org/I4210106610"]}],"countries":["IS"],"is_corresponding":false,"raw_author_name":"Antonio Di Lieto","raw_affiliation_strings":["Mental Health Services, Landspitali University Hospital , 101 Reykjavik, Iceland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mental Health Services, Landspitali University Hospital , 101 Reykjavik, Iceland","institution_ids":["https://openalex.org/I4210106610"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073379520","display_name":"Jari Yli\u2010Kauhaluoma","orcid":"https://orcid.org/0000-0003-0370-7653"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Jari Yli-Kauhaluoma","raw_affiliation_strings":["Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki , 00790 Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki , 00790 Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003994395","display_name":"Henri Xhaard","orcid":"https://orcid.org/0000-0002-3000-7858"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Henri Xhaard","raw_affiliation_strings":["Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki , 00790 Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki , 00790 Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101807666","display_name":"Antonio Federico","orcid":"https://orcid.org/0000-0003-2554-9879"},"institutions":[{"id":"https://openalex.org/I166825849","display_name":"Tampere University","ror":"https://ror.org/033003e23","country_code":"FI","type":"education","lineage":["https://openalex.org/I166825849"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Antonio Federico","raw_affiliation_strings":["BioMediTech Institute, Tampere University , 33520 Tampere, Finland","Faculty of Medicine and Health Technology, Tampere University , 33520 Tampere, Finland","Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE) , 33520 Tampere, Finland","Tampere Institute for Advanced Study , 33520 Tampere, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioMediTech Institute, Tampere University , 33520 Tampere, Finland","institution_ids":["https://openalex.org/I166825849"]},{"raw_affiliation_string":"Faculty of Medicine and Health Technology, Tampere University , 33520 Tampere, Finland","institution_ids":["https://openalex.org/I166825849"]},{"raw_affiliation_string":"Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE) , 33520 Tampere, Finland","institution_ids":[]},{"raw_affiliation_string":"Tampere Institute for Advanced Study , 33520 Tampere, Finland","institution_ids":["https://openalex.org/I166825849"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041632230","display_name":"Angela Serra","orcid":"https://orcid.org/0000-0002-3374-1492"},"institutions":[{"id":"https://openalex.org/I166825849","display_name":"Tampere University","ror":"https://ror.org/033003e23","country_code":"FI","type":"education","lineage":["https://openalex.org/I166825849"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Angela Serra","raw_affiliation_strings":["BioMediTech Institute, Tampere University , 33520 Tampere, Finland","Faculty of Medicine and Health Technology, Tampere University , 33520 Tampere, Finland","Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE) , 33520 Tampere, Finland","Tampere Institute for Advanced Study , 33520 Tampere, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioMediTech Institute, Tampere University , 33520 Tampere, Finland","institution_ids":["https://openalex.org/I166825849"]},{"raw_affiliation_string":"Faculty of Medicine and Health Technology, Tampere University , 33520 Tampere, Finland","institution_ids":["https://openalex.org/I166825849"]},{"raw_affiliation_string":"Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE) , 33520 Tampere, Finland","institution_ids":[]},{"raw_affiliation_string":"Tampere Institute for Advanced Study , 33520 Tampere, Finland","institution_ids":["https://openalex.org/I166825849"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028682033","display_name":"Dario Greco","orcid":"https://orcid.org/0000-0001-9195-9003"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I166825849","display_name":"Tampere University","ror":"https://ror.org/033003e23","country_code":"FI","type":"education","lineage":["https://openalex.org/I166825849"]},{"id":"https://openalex.org/I2800229700","display_name":"Helsinki Institute of Physics","ror":"https://ror.org/01x2x1522","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I2800229700","https://openalex.org/I63548447","https://openalex.org/I94722563","https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Dario Greco","raw_affiliation_strings":["BioMediTech Institute, Tampere University , 33520 Tampere, Finland","Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki , 00790 Helsinki, Finland","Faculty of Medicine and Health Technology, Tampere University , 33520 Tampere, Finland","Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE) , 33520 Tampere, Finland","Institute of Biotechnology, University of Helsinki , 00790 Helsinki, Finland"],"raw_orcid":"https://orcid.org/0000-0001-9195-9003","affiliations":[{"raw_affiliation_string":"BioMediTech Institute, Tampere University , 33520 Tampere, Finland","institution_ids":["https://openalex.org/I166825849"]},{"raw_affiliation_string":"Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki , 00790 Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]},{"raw_affiliation_string":"Faculty of Medicine and Health Technology, Tampere University , 33520 Tampere, Finland","institution_ids":["https://openalex.org/I166825849"]},{"raw_affiliation_string":"Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE) , 33520 Tampere, Finland","institution_ids":[]},{"raw_affiliation_string":"Institute of Biotechnology, University of Helsinki , 00790 Helsinki, Finland","institution_ids":["https://openalex.org/I133731052","https://openalex.org/I2800229700"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5028682033"],"corresponding_institution_ids":["https://openalex.org/I133731052","https://openalex.org/I166825849","https://openalex.org/I2800229700"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":4574,"currency":"EUR","value_usd":4933},"fwci":0.0927,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.3910504,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"39","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6953999996185303,"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":0.6953999996185303,"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":0.13830000162124634,"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/T10885","display_name":"Gene expression and cancer classification","score":0.06430000066757202,"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":0.6932513117790222},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.5762543678283691},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5551217794418335},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.48902806639671326},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32503601908683777},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1835540235042572},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1285855770111084},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.108396977186203},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.08627718687057495},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08417928218841553}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6932513117790222},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5762543678283691},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5551217794418335},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.48902806639671326},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32503601908683777},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1835540235042572},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1285855770111084},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.108396977186203},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08627718687057495},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08417928218841553}],"mesh":[{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btad341","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad341","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad341/50439486/btad341.pdf","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:37225400","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37225400","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:10243850","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10243850","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10243850/pdf/btad341.pdf","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"},{"id":"pmh:oai:opinvisindi.is:20.500.11815/4417","is_oa":true,"landing_page_url":"https://hdl.handle.net/20.500.11815/4417","pdf_url":null,"source":{"id":"https://openalex.org/S4306401866","display_name":"Opin v\u00edsindi (Opin v\u00edsindi)","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"/dk/atira/pure/researchoutput/researchoutputtypes/contributiontojournal/article"},{"id":"pmh:oai:trepo.tuni.fi:10024/208711","is_oa":true,"landing_page_url":"https://trepo.tuni.fi/handle/10024/208711","pdf_url":null,"source":{"id":"https://openalex.org/S4306401860","display_name":"Tampere University Institutional Repository (Tampere University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I150589677","host_organization_name":"Tampere University of Applied Sciences","host_organization_lineage":["https://openalex.org/I150589677"],"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":null,"raw_type":"publishedVersion"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad341","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad341","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad341/50439486/btad341.pdf","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/G5445264010","display_name":null,"funder_award_id":"322761","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"}],"funders":[{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"},{"id":"https://openalex.org/F4320338335","display_name":"H2020 European Research Council","ror":"https://ror.org/0472cxd90"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4377941318.pdf"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W2044692345","https://openalex.org/W2046678194","https://openalex.org/W2054725011","https://openalex.org/W2099892456","https://openalex.org/W2118993986","https://openalex.org/W2121604817","https://openalex.org/W2130410032","https://openalex.org/W2146512944","https://openalex.org/W2605370598","https://openalex.org/W2612467560","https://openalex.org/W2763420753","https://openalex.org/W2767281692","https://openalex.org/W2803221166","https://openalex.org/W2883968630","https://openalex.org/W2884724578","https://openalex.org/W2889250103","https://openalex.org/W2899015035","https://openalex.org/W2899070097","https://openalex.org/W2908199103","https://openalex.org/W2999903252","https://openalex.org/W3003257820","https://openalex.org/W3014118352","https://openalex.org/W3015334569","https://openalex.org/W3016893324","https://openalex.org/W3023855676","https://openalex.org/W3032071647","https://openalex.org/W3048864164","https://openalex.org/W3092977177","https://openalex.org/W3100661518","https://openalex.org/W3103145119","https://openalex.org/W3112600195","https://openalex.org/W3119357010","https://openalex.org/W3126541761","https://openalex.org/W3135303713","https://openalex.org/W3197044966","https://openalex.org/W3198724606","https://openalex.org/W4200555798","https://openalex.org/W4210522554","https://openalex.org/W4224239606","https://openalex.org/W4226036563","https://openalex.org/W4282839013","https://openalex.org/W4283738507","https://openalex.org/W4289274885","https://openalex.org/W4294647273","https://openalex.org/W4318476889","https://openalex.org/W6754360973"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2399513595","https://openalex.org/W4388386498","https://openalex.org/W2028462563","https://openalex.org/W2390279801","https://openalex.org/W2942994004","https://openalex.org/W2982720988","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W3155641129"],"abstract_inverted_index":{"MOTIVATION:":[0],"Transcriptomic":[1],"data":[2,19,241],"can":[3,56],"be":[4,22],"used":[5,74],"to":[6,21,26,75,142,150,159,167,220],"describe":[7],"the":[8,29,41,66,72,85,88,122,169,174,192,207,211,233,243],"mechanism":[9],"of":[10,13,31,43,50,99,113,178,223],"action":[11],"(MOA)":[12],"a":[14,92,118],"chemical":[15],"compound.":[16],"However,":[17],"omics":[18],"tend":[20],"complex":[23],"and":[24,61,82,134,242,250],"prone":[25,158],"noise,":[27],"making":[28],"comparison":[30,98],"different":[32],"datasets":[33],"challenging.":[34],"Often,":[35],"transcriptomic":[36,100],"profiles":[37,101,209],"are":[38,214],"compared":[39],"at":[40],"level":[42],"individual":[44,123],"gene":[45,77,124,136,175],"expression":[46,78,176,208],"values,":[47],"or":[48,71],"sets":[49,222],"differentially":[51],"expressed":[52],"genes.":[53,89],"Such":[54],"approaches":[55],"suffer":[57],"from":[58],"underlying":[59],"technical":[60,80],"biological":[62,67,212,235],"variance,":[63],"such":[64],"as":[65,153,155,189,191],"system":[68],"exposed":[69,231],"on":[70,110,232],"machine/method":[73],"measure":[76],"data,":[79],"errors":[81],"further":[83],"neglect":[84],"relationships":[86],"between":[87],"We":[90,164],"propose":[91],"network":[93],"mapping":[94],"approach":[95],"for":[96],"knowledge-driven":[97],"(KNeMAP),":[102],"which":[103],"combines":[104],"genes":[105],"into":[106],"similarity":[107],"groups":[108],"based":[109,133],"multiple":[111],"levels":[112],"prior":[114,151],"information,":[115],"hence":[116],"adding":[117],"higher-level":[119],"view":[120],"onto":[121],"view.":[125],"When":[126],"comparing":[127],"KNeMAP":[128,139,166,217,244],"with":[129,145,148,186,201],"fold":[130],"change":[131],"(expression)":[132],"deregulated":[135],"set-based":[137],"methods,":[138],"was":[140,218],"able":[141,219],"group":[143],"compounds":[144,224],"higher":[146],"accuracy":[147],"respect":[149],"information":[152],"well":[154,190],"is":[156,246],"less":[157],"noise":[160],"corrupted":[161],"data.":[162],"RESULT:":[163],"applied":[165],"analyze":[168],"Connectivity":[170],"Map":[171],"dataset,":[172],"where":[173,197],"changes":[177],"three":[179],"cell":[180,199],"lines":[181,200],"were":[182,204],"analyzed":[183],"after":[184],"treatment":[185],"676":[187],"drugs":[188],"Fortino":[193],"et":[194],"al.":[195],"dataset":[196],"two":[198],"31":[202],"nanomaterials":[203],"analyzed.":[205],"Although":[206],"across":[210],"systems":[213],"highly":[215],"different,":[216],"identify":[221],"that":[225],"induce":[226],"similar":[227],"molecular":[228],"responses":[229],"when":[230],"same":[234],"system.":[236],"AVAILABILITY":[237],"AND":[238],"IMPLEMENTATION:":[239],"Relevant":[240],"function":[245],"available":[247],"at:":[248],"https://github.com/fhaive/KNeMAP":[249],"10.5281/zenodo.7334711.":[251]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}