{"id":"https://openalex.org/W4390789325","doi":"https://doi.org/10.1186/s12859-024-05632-w","title":"Robustness evaluations of pathway activity inference methods on gene expression data","display_name":"Robustness evaluations of pathway activity inference methods on gene expression data","publication_year":2024,"publication_date":"2024-01-12","ids":{"openalex":"https://openalex.org/W4390789325","doi":"https://doi.org/10.1186/s12859-024-05632-w","pmid":"https://pubmed.ncbi.nlm.nih.gov/38216898"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-024-05632-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05632-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05632-w","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/s12859-024-05632-w","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049485265","display_name":"Tay Xin Hui","orcid":"https://orcid.org/0009-0007-0016-7555"},"institutions":[{"id":"https://openalex.org/I930072361","display_name":"Tun Hussein Onn University of Malaysia","ror":"https://ror.org/01c5wha71","country_code":"MY","type":"education","lineage":["https://openalex.org/I930072361"]}],"countries":["MY"],"is_corresponding":false,"raw_author_name":"Tay Xin Hui","raw_affiliation_strings":["Soft Computing and Data Mining Center, Faculty of Computer Sciences and Information Technology, Universiti Tun Hussein Onn Malaysia (UTHM), 83000, Batu Pahat, Malaysia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Soft Computing and Data Mining Center, Faculty of Computer Sciences and Information Technology, Universiti Tun Hussein Onn Malaysia (UTHM), 83000, Batu Pahat, Malaysia","institution_ids":["https://openalex.org/I930072361"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064913575","display_name":"Shahreen Kasim","orcid":"https://orcid.org/0000-0002-4180-4377"},"institutions":[{"id":"https://openalex.org/I930072361","display_name":"Tun Hussein Onn University of Malaysia","ror":"https://ror.org/01c5wha71","country_code":"MY","type":"education","lineage":["https://openalex.org/I930072361"]}],"countries":["MY"],"is_corresponding":true,"raw_author_name":"Shahreen Kasim","raw_affiliation_strings":["Soft Computing and Data Mining Center, Faculty of Computer Sciences and Information Technology, Universiti Tun Hussein Onn Malaysia (UTHM), 83000, Batu Pahat, Malaysia. shahreen@uthm.edu.my","Soft Computing and Data Mining Center, Faculty of Computer Sciences and Information Technology, Universiti Tun Hussein Onn Malaysia (UTHM), 83000, Batu Pahat, Malaysia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Soft Computing and Data Mining Center, Faculty of Computer Sciences and Information Technology, Universiti Tun Hussein Onn Malaysia (UTHM), 83000, Batu Pahat, Malaysia. shahreen@uthm.edu.my","institution_ids":["https://openalex.org/I930072361"]},{"raw_affiliation_string":"Soft Computing and Data Mining Center, Faculty of Computer Sciences and Information Technology, Universiti Tun Hussein Onn Malaysia (UTHM), 83000, Batu Pahat, Malaysia","institution_ids":["https://openalex.org/I930072361"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011080351","display_name":"Izzatdin Abdul Aziz","orcid":"https://orcid.org/0000-0003-2654-4463"},"institutions":[{"id":"https://openalex.org/I203899302","display_name":"Universiti Teknologi Petronas","ror":"https://ror.org/048g2sh07","country_code":"MY","type":"education","lineage":["https://openalex.org/I203899302"]}],"countries":["MY"],"is_corresponding":false,"raw_author_name":"Izzatdin Abdul Aziz","raw_affiliation_strings":["Computer and Information Sciences Department (CISD), Universiti Teknologi PETRONAS (UTP), 32610, Seri Iskandar, Malaysia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer and Information Sciences Department (CISD), Universiti Teknologi PETRONAS (UTP), 32610, Seri Iskandar, Malaysia","institution_ids":["https://openalex.org/I203899302"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029675423","display_name":"Mohd Farhan Md Fudzee","orcid":"https://orcid.org/0000-0002-6801-2660"},"institutions":[{"id":"https://openalex.org/I930072361","display_name":"Tun Hussein Onn University of Malaysia","ror":"https://ror.org/01c5wha71","country_code":"MY","type":"education","lineage":["https://openalex.org/I930072361"]}],"countries":["MY"],"is_corresponding":false,"raw_author_name":"Mohd Farhan Md Fudzee","raw_affiliation_strings":["Soft Computing and Data Mining Center, Faculty of Computer Sciences and Information Technology, Universiti Tun Hussein Onn Malaysia (UTHM), 83000, Batu Pahat, Malaysia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Soft Computing and Data Mining Center, Faculty of Computer Sciences and Information Technology, Universiti Tun Hussein Onn Malaysia (UTHM), 83000, Batu Pahat, Malaysia","institution_ids":["https://openalex.org/I930072361"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034902288","display_name":"Nazleeni Samiha Haron","orcid":"https://orcid.org/0000-0002-8028-3033"},"institutions":[{"id":"https://openalex.org/I203899302","display_name":"Universiti Teknologi Petronas","ror":"https://ror.org/048g2sh07","country_code":"MY","type":"education","lineage":["https://openalex.org/I203899302"]}],"countries":["MY"],"is_corresponding":false,"raw_author_name":"Nazleeni Samiha Haron","raw_affiliation_strings":["Computer and Information Sciences Department (CISD), Universiti Teknologi PETRONAS (UTP), 32610, Seri Iskandar, Malaysia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer and Information Sciences Department (CISD), Universiti Teknologi PETRONAS (UTP), 32610, Seri Iskandar, Malaysia","institution_ids":["https://openalex.org/I203899302"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059360335","display_name":"Tole Sutikno","orcid":"https://orcid.org/0000-0002-1595-2915"},"institutions":[{"id":"https://openalex.org/I2608206482","display_name":"Universitas Ahmad Dahlan","ror":"https://ror.org/03hn13397","country_code":"ID","type":"education","lineage":["https://openalex.org/I2608206482"]}],"countries":["ID"],"is_corresponding":false,"raw_author_name":"Tole Sutikno","raw_affiliation_strings":["Department of Electrical Engineering, Universitas Ahmad Dahlan (UAD), 55166, Yogyakarta, Indonesia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, Universitas Ahmad Dahlan (UAD), 55166, Yogyakarta, Indonesia","institution_ids":["https://openalex.org/I2608206482"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103969789","display_name":"Rohayanti Hassan","orcid":null},"institutions":[{"id":"https://openalex.org/I4576418","display_name":"University of Technology Malaysia","ror":"https://ror.org/026w31v75","country_code":"MY","type":"education","lineage":["https://openalex.org/I4576418"]}],"countries":["MY"],"is_corresponding":false,"raw_author_name":"Rohayanti Hassan","raw_affiliation_strings":["Faculty of Electrical Engineering, Universiti Teknologi Malaysia (UTM), 81310, Johor Bahru, Malaysia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Electrical Engineering, Universiti Teknologi Malaysia (UTM), 81310, Johor Bahru, Malaysia","institution_ids":["https://openalex.org/I4576418"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057640595","display_name":"Hairulnizam Mahdin","orcid":"https://orcid.org/0000-0002-2275-0094"},"institutions":[{"id":"https://openalex.org/I930072361","display_name":"Tun Hussein Onn University of Malaysia","ror":"https://ror.org/01c5wha71","country_code":"MY","type":"education","lineage":["https://openalex.org/I930072361"]}],"countries":["MY"],"is_corresponding":false,"raw_author_name":"Hairulnizam Mahdin","raw_affiliation_strings":["Soft Computing and Data Mining Center, Faculty of Computer Sciences and Information Technology, Universiti Tun Hussein Onn Malaysia (UTHM), 83000, Batu Pahat, Malaysia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Soft Computing and Data Mining Center, Faculty of Computer Sciences and Information Technology, Universiti Tun Hussein Onn Malaysia (UTHM), 83000, Batu Pahat, Malaysia","institution_ids":["https://openalex.org/I930072361"]}]},{"author_position":"last","author":{"id":null,"display_name":"Seah Choon Sen","orcid":null},"institutions":[{"id":"https://openalex.org/I4576418","display_name":"University of Technology Malaysia","ror":"https://ror.org/026w31v75","country_code":"MY","type":"education","lineage":["https://openalex.org/I4576418"]}],"countries":["MY"],"is_corresponding":false,"raw_author_name":"Seah Choon Sen","raw_affiliation_strings":["Faculty of Computing, Universiti Teknologi Malaysia (UTM), 81310, Johor Bahru, Malaysia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computing, Universiti Teknologi Malaysia (UTM), 81310, Johor Bahru, Malaysia","institution_ids":["https://openalex.org/I4576418"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5064913575"],"corresponding_institution_ids":["https://openalex.org/I930072361"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.6029,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.64869006,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"25","issue":"1","first_page":"23","last_page":"23"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9621000289916992,"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":0.9621000289916992,"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/T10885","display_name":"Gene expression and cancer classification","score":0.010999999940395355,"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":0.004000000189989805,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.8296111822128296},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.8032939434051514},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5309317111968994},{"id":"https://openalex.org/keywords/reproducibility","display_name":"Reproducibility","score":0.4490174651145935},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4486350417137146},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39829719066619873},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3431869447231293},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3223755657672882},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.29466569423675537},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28730911016464233},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.21395689249038696},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.19125553965568542},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13103199005126953}],"concepts":[{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.8296111822128296},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.8032939434051514},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5309317111968994},{"id":"https://openalex.org/C9893847","wikidata":"https://www.wikidata.org/wiki/Q1425625","display_name":"Reproducibility","level":2,"score":0.4490174651145935},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4486350417137146},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39829719066619873},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3431869447231293},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3223755657672882},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.29466569423675537},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28730911016464233},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21395689249038696},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.19125553965568542},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13103199005126953}],"mesh":[{"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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-024-05632-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05632-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05632-w","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:38216898","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38216898","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:10785356","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10785356","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10785356/pdf/12859_2024_Article_5632.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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:63e7d008de894a00913f61666e7ae209","is_oa":true,"landing_page_url":"https://doaj.org/article/63e7d008de894a00913f61666e7ae209","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 25, Iss 1, Pp 1-24 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-024-05632-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05632-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05632-w","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":[],"awards":[{"id":"https://openalex.org/G4025999432","display_name":null,"funder_award_id":"015LC0-353","funder_id":"https://openalex.org/F4320329394","funder_display_name":"Yayasan UTP"},{"id":"https://openalex.org/G7448000900","display_name":null,"funder_award_id":"015LC0-353","funder_id":"https://openalex.org/F4320323380","funder_display_name":"Universiti Teknologi Petronas"}],"funders":[{"id":"https://openalex.org/F4320310112","display_name":"Universiti Tun Hussein Onn Malaysia","ror":"https://ror.org/01c5wha71"},{"id":"https://openalex.org/F4320323380","display_name":"Universiti Teknologi Petronas","ror":"https://ror.org/048g2sh07"},{"id":"https://openalex.org/F4320329394","display_name":"Yayasan UTP","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4390789325.pdf"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W1607267312","https://openalex.org/W1620997626","https://openalex.org/W1848567445","https://openalex.org/W1970156673","https://openalex.org/W1978545732","https://openalex.org/W1989277387","https://openalex.org/W1992045522","https://openalex.org/W1999842873","https://openalex.org/W2010502047","https://openalex.org/W2025657174","https://openalex.org/W2046759180","https://openalex.org/W2058237157","https://openalex.org/W2084533385","https://openalex.org/W2096766502","https://openalex.org/W2097554668","https://openalex.org/W2100980426","https://openalex.org/W2102074241","https://openalex.org/W2109103446","https://openalex.org/W2109912704","https://openalex.org/W2119387367","https://openalex.org/W2122863959","https://openalex.org/W2128814129","https://openalex.org/W2130410032","https://openalex.org/W2136629313","https://openalex.org/W2140416663","https://openalex.org/W2142720308","https://openalex.org/W2146995322","https://openalex.org/W2156782835","https://openalex.org/W2158384363","https://openalex.org/W2159478099","https://openalex.org/W2159482845","https://openalex.org/W2159707944","https://openalex.org/W2161818848","https://openalex.org/W2165011536","https://openalex.org/W2167119716","https://openalex.org/W2167971649","https://openalex.org/W2224812643","https://openalex.org/W2234559012","https://openalex.org/W2263356566","https://openalex.org/W2577621264","https://openalex.org/W2663330219","https://openalex.org/W2769019754","https://openalex.org/W2790711259","https://openalex.org/W2807134042","https://openalex.org/W2912198494","https://openalex.org/W2949066452","https://openalex.org/W2979832776","https://openalex.org/W2998150256","https://openalex.org/W3015749343","https://openalex.org/W3039150496","https://openalex.org/W3215626765","https://openalex.org/W4226298065","https://openalex.org/W4233698560","https://openalex.org/W4294216483","https://openalex.org/W4322503786","https://openalex.org/W4399588400"],"related_works":["https://openalex.org/W2413717610","https://openalex.org/W1973270181","https://openalex.org/W2417696084","https://openalex.org/W2368782778","https://openalex.org/W2087830269","https://openalex.org/W3106281778","https://openalex.org/W2140154150","https://openalex.org/W638612878","https://openalex.org/W4324138256","https://openalex.org/W2083330954"],"abstract_inverted_index":{"BACKGROUND:":[0],"With":[1],"the":[2,49,64,99,110,116,144,147,159,176,185,188],"exponential":[3],"growth":[4],"of":[5,58,66,77,101,118,134,151,161],"high-throughput":[6],"technologies,":[7],"multiple":[8],"pathway":[9,17,24,81,102,105,152,162],"analysis":[10],"methods":[11,27,84,155,173,194,203],"have":[12],"been":[13],"proposed":[14],"to":[15,97,114,206,220],"estimate":[16],"activities":[18],"from":[19,51],"gene":[20],"expression":[21],"profiles.":[22],"These":[23],"activity":[25,82,103,106,153],"inference":[26,83,107,154],"can":[28],"be":[29],"divided":[30],"into":[31],"two":[32,91],"main":[33],"categories:":[34],"non-Topology-Based":[35],"(non-TB)":[36],"and":[37,45,61,121,131,138,214],"Pathway":[38],"Topology-Based":[39],"(PTB)":[40],"methods.":[41,126,222],"Although":[42],"some":[43],"review":[44],"survey":[46],"articles":[47],"discussed":[48],"topic":[50],"different":[52],"aspects,":[53],"there":[54],"is":[55],"a":[56],"lack":[57],"systematic":[59],"assessment":[60,95,112,190],"comparisons":[62],"on":[63,90,143],"robustness":[65,75,100,117],"these":[67,125],"approaches.":[68],"RESULTS:":[69],"Thus,":[70],"this":[71],"study":[72],"presents":[73],"comprehensive":[74],"evaluations":[76],"seven":[78],"widely":[79],"used":[80],"using":[85],"six":[86],"cancer":[87,182,217],"datasets":[88],"based":[89],"assessments.":[92],"The":[93,127],"first":[94,145],"seeks":[96],"investigate":[98],"in":[104,174,209],"methods,":[108],"while":[109],"second":[111,189],"aims":[113],"assess":[115],"risk-active":[119],"pathways":[120,137],"genes":[122,139],"predicted":[123],"by":[124],"mean":[128,148],"reproducibility":[129,149,178,212],"power":[130,150,179,213],"total":[132],"number":[133,160],"identified":[135],"informative":[136],"were":[140],"evaluated.":[141],"Based":[142],"assessment,":[146],"generally":[156,204],"decreased":[157],"as":[158],"selections":[163],"increased.":[164],"Entropy-based":[165],"Directed":[166],"Random":[167],"Walk":[168],"(e-DRW)":[169],"distinctly":[170],"outperformed":[171],"other":[172,186],"exhibiting":[175],"greatest":[177],"across":[180,198],"all":[181],"datasets.":[183,199],"On":[184],"hand,":[187],"shows":[191],"that":[192],"no":[193],"provide":[195],"satisfactory":[196],"results":[197],"CONCLUSION:":[200],"However,":[201],"PTB":[202],"appear":[205],"perform":[207],"better":[208],"producing":[210],"greater":[211],"identifying":[215],"potential":[216],"markers":[218],"compared":[219],"non-TB":[221]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2024,"cited_by_count":1}],"updated_date":"2026-06-17T06:14:20.161405","created_date":"2025-10-10T00:00:00"}
