{"id":"https://openalex.org/W3045128410","doi":"https://doi.org/10.1109/access.2020.3010796","title":"Signaling Pathway Analysis Combined With the Strength Variations of Interactions Between Genes Under Different Conditions","display_name":"Signaling Pathway Analysis Combined With the Strength Variations of Interactions Between Genes Under Different Conditions","publication_year":2020,"publication_date":"2020-01-01","ids":{"openalex":"https://openalex.org/W3045128410","doi":"https://doi.org/10.1109/access.2020.3010796","mag":"3045128410"},"language":"en","primary_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2020.3010796","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/8948470/09145531.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},"type":"article","type_crossref":"journal-article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://ieeexplore.ieee.org/ielx7/6287639/8948470/09145531.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026952692","display_name":"Zhenshen Bao","orcid":"https://orcid.org/0000-0002-6376-7124"},"institutions":[{"id":"https://openalex.org/I4387154005","display_name":"State Key Laboratory of Digital Medical Engineering","ror":"https://ror.org/03ab0at74","country_code":null,"type":"facility","lineage":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]},{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhenshen Bao","raw_affiliation_strings":["State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, China","institution_ids":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101993812","display_name":"Yihua Zhu","orcid":"https://orcid.org/0000-0003-2491-669X"},"institutions":[{"id":"https://openalex.org/I119454577","display_name":"Nanjing Agricultural University","ror":"https://ror.org/05td3s095","country_code":"CN","type":"education","lineage":["https://openalex.org/I119454577"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yihua Zhu","raw_affiliation_strings":["College of Information Science and Technology, Nanjing Agricultural University, Nanjing, China"],"affiliations":[{"raw_affiliation_string":"College of Information Science and Technology, Nanjing Agricultural University, Nanjing, China","institution_ids":["https://openalex.org/I119454577"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078457745","display_name":"Qinyu Ge","orcid":null},"institutions":[{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]},{"id":"https://openalex.org/I4387154005","display_name":"State Key Laboratory of Digital Medical Engineering","ror":"https://ror.org/03ab0at74","country_code":null,"type":"facility","lineage":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qinyu Ge","raw_affiliation_strings":["State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, China","institution_ids":["https://openalex.org/I76569877","https://openalex.org/I4387154005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102781094","display_name":"Wanjun Gu","orcid":"https://orcid.org/0000-0003-4501-0539"},"institutions":[{"id":"https://openalex.org/I4387154005","display_name":"State Key Laboratory of Digital Medical Engineering","ror":"https://ror.org/03ab0at74","country_code":null,"type":"facility","lineage":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]},{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wanjun Gu","raw_affiliation_strings":["State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, China","institution_ids":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053690577","display_name":"Xianjun Dong","orcid":"https://orcid.org/0000-0002-8052-9320"},"institutions":[{"id":"https://openalex.org/I1321296531","display_name":"National Institute of Standards and Technology","ror":"https://ror.org/05xpvk416","country_code":"US","type":"government","lineage":["https://openalex.org/I1321296531","https://openalex.org/I1343035065"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I1283280774","display_name":"Brigham and Women's Hospital","ror":"https://ror.org/04b6nzv94","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1283280774","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xianjun Dong","raw_affiliation_strings":["Department of Neurology, Harvard Medical School, Boston, USA","National Institute of Standards and Technology, Boulder, USA","Neurogenomics Laboratory and Precision Neurology Program, Brigham and Women's Hospital, Boston, USA"],"affiliations":[{"raw_affiliation_string":"National Institute of Standards and Technology, Boulder, USA","institution_ids":["https://openalex.org/I1321296531"]},{"raw_affiliation_string":"Department of Neurology, Harvard Medical School, Boston, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Neurogenomics Laboratory and Precision Neurology Program, Brigham and Women's Hospital, Boston, USA","institution_ids":["https://openalex.org/I1283280774"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042168221","display_name":"Yunfei Bai","orcid":"https://orcid.org/0000-0002-4088-4117"},"institutions":[{"id":"https://openalex.org/I4387154005","display_name":"State Key Laboratory of Digital Medical Engineering","ror":"https://ror.org/03ab0at74","country_code":null,"type":"facility","lineage":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]},{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yunfei Bai","raw_affiliation_strings":["State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, China","institution_ids":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]}]}],"institution_assertions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1850,"currency":"USD","value_usd":1850,"provenance":"doaj"},"apc_paid":{"value":1850,"currency":"USD","value_usd":1850,"provenance":"doaj"},"fwci":0.315,"has_fulltext":true,"fulltext_origin":"pdf","cited_by_count":5,"citation_normalized_percentile":{"value":0.690713,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":79,"max":81},"biblio":{"volume":"8","issue":null,"first_page":"138036","last_page":"138045"},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9999,"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":0.9999,"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":0.9951,"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":0.9858,"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/prioritization","display_name":"Prioritization","score":0.5638884},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.4853922},{"id":"https://openalex.org/keywords/biological-pathway","display_name":"Biological pathway","score":0.4655816}],"concepts":[{"id":"https://openalex.org/C2777615720","wikidata":"https://www.wikidata.org/wiki/Q11888847","display_name":"Prioritization","level":2,"score":0.5638884},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.54106784},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.51448154},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.4853922},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4782742},{"id":"https://openalex.org/C9927688","wikidata":"https://www.wikidata.org/wiki/Q4915012","display_name":"Biological pathway","level":4,"score":0.4655816},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3909576},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.30259752},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.23742324},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2020.3010796","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/8948470/09145531.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":false,"landing_page_url":"https://doaj.org/article/3b4145391a334d06be712d66231b026d","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":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2020.3010796","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/8948470/09145531.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.75,"display_name":"Good health and well-being"}],"grants":[{"funder":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China","award_id":"61271055"},{"funder":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China","award_id":"61471112"},{"funder":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China","award_id":"61871121"}],"datasets":[],"versions":[],"referenced_works_count":69,"referenced_works":["https://openalex.org/W1417555467","https://openalex.org/W1512072225","https://openalex.org/W1595610987","https://openalex.org/W1618390401","https://openalex.org/W1849111649","https://openalex.org/W1919452523","https://openalex.org/W1966752541","https://openalex.org/W1972755526","https://openalex.org/W1978723648","https://openalex.org/W1985512433","https://openalex.org/W1986501321","https://openalex.org/W1988263223","https://openalex.org/W1988275221","https://openalex.org/W1996667997","https://openalex.org/W1998902445","https://openalex.org/W2007012192","https://openalex.org/W2011417152","https://openalex.org/W2011696346","https://openalex.org/W2016542388","https://openalex.org/W2018257233","https://openalex.org/W2018340043","https://openalex.org/W2020242768","https://openalex.org/W2020859582","https://openalex.org/W2021116504","https://openalex.org/W2044545697","https://openalex.org/W2046875228","https://openalex.org/W2050245934","https://openalex.org/W2050751022","https://openalex.org/W2058125715","https://openalex.org/W2060689128","https://openalex.org/W2084533385","https://openalex.org/W2089390825","https://openalex.org/W2096561521","https://openalex.org/W2098021159","https://openalex.org/W2100980426","https://openalex.org/W2110687686","https://openalex.org/W2113676124","https://openalex.org/W2113764711","https://openalex.org/W2114729479","https://openalex.org/W2129099812","https://openalex.org/W2129466727","https://openalex.org/W2130410032","https://openalex.org/W2135056923","https://openalex.org/W2135891958","https://openalex.org/W2136159134","https://openalex.org/W2138485734","https://openalex.org/W2146026944","https://openalex.org/W2147714160","https://openalex.org/W2148092441","https://openalex.org/W2155330008","https://openalex.org/W2158240093","https://openalex.org/W2159482845","https://openalex.org/W2189484097","https://openalex.org/W2196971464","https://openalex.org/W2235123180","https://openalex.org/W2332308455","https://openalex.org/W2336690572","https://openalex.org/W2338992976","https://openalex.org/W2398534503","https://openalex.org/W2398800029","https://openalex.org/W2565584054","https://openalex.org/W2767446875","https://openalex.org/W2803548822","https://openalex.org/W2885688533","https://openalex.org/W2901329784","https://openalex.org/W2944851004","https://openalex.org/W2968022676","https://openalex.org/W4242404314","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W4321353415","https://openalex.org/W4283209547","https://openalex.org/W2745001401","https://openalex.org/W2506292322","https://openalex.org/W2378211422","https://openalex.org/W2157193718","https://openalex.org/W2151866902","https://openalex.org/W2130974462","https://openalex.org/W2120108543","https://openalex.org/W2046406569"],"abstract_inverted_index":{"Signaling":[0],"pathway":[1,24,45,89],"analysis":[2,46,90],"has":[3],"become":[4],"a":[5,29,63,110],"routine":[6],"task":[7],"after":[8,91],"differentially":[9],"expressed":[10],"gene":[11,114],"(DEG)":[12],"studies":[13],"across":[14],"disease":[15],"conditions,":[16],"drug":[17],"treatments,":[18],"or":[19],"developmental":[20],"stages.":[21],"A":[22],"signaling":[23,44,55,81,88],"can":[25,211,226],"be":[26,227],"represented":[27],"by":[28,108],"graph":[30],"that":[31,140],"consists":[32],"of":[33,52,76,99,112,129,148,156,167,171,178,191,216,224],"Genes":[34],"and":[35,122,150],"interactions":[36,53,203],"(the":[37],"genetic":[38],"regulation)":[39],"between":[40,78],"them.":[41],"However,":[42],"existing":[43],"methods":[47,107],"ignore":[48],"the":[49,73,97,143,151,160,168,172,176,184,188,192,199,214,217],"strength":[50,74,189,206],"variations":[51,75,207],"in":[54,80,117,146,154,165],"pathways":[56,82],"under":[57,83,208],"different":[58,84,209],"conditions.":[59],"Here,":[60],"we":[61,101],"developed":[62],"novel":[64],"method":[65,145,153,162],"named":[66],"SPACI":[67,103,130,141,158,179,225],"(Signaling":[68],"Pathway":[69],"Analysis":[70],"Combined":[71],"with":[72,104,134,183,198,204],"Interactions":[77],"genes":[79],"conditions)":[85],"to":[86],"improve":[87,213],"DEG":[92],"studies.":[93],"To":[94],"further":[95],"evaluate":[96],"performance":[98],"SPACI,":[100],"compared":[102,133,164,182],"nine":[105],"other":[106],"using":[109],"benchmark":[111],"28":[113],"expression":[115],"datasets":[116],"two":[118,173],"standard":[119],"measures:":[120],"sensitivity":[121],"prioritization.":[123],"The":[124,137,202,221],"False":[125],"positive":[126],"rate":[127],"(FPR)":[128],"was":[131],"also":[132],"five":[135],"methods.":[136,186],"results":[138],"show":[139],"is":[142,159,180,194],"second-ranked":[144],"terms":[147,155,166],"prioritization":[149],"third-ranked":[152],"sensitivity.":[157],"top":[161],"when":[163],"sum":[169],"value":[170],"ranks.":[174],"Also,":[175],"FPR":[177],"modest":[181],"classic":[185],"Furthermore,":[187],"variation":[190],"interaction":[193],"demonstrated":[195],"as":[196],"coherent":[197],"biological":[200,219],"problem.":[201],"high":[205],"conditions":[210],"help":[212],"discovery":[215],"underlying":[218],"information.":[220],"R":[222],"package":[223],"accessed":[228],"at":[229],"https://github.com/ZhenshenBao/SPACI.":[230]},"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W3045128410","counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2024-12-15T02:47:30.302724","created_date":"2020-07-29"}