{"id":"https://openalex.org/W7117161823","doi":"https://doi.org/10.1021/acs.jcim.5c02226","title":"DeepMLP: A Proteomics-Driven Deep Learning Framework for Identifying Mis-Localized Proteins across Pan-Cancer","display_name":"DeepMLP: A Proteomics-Driven Deep Learning Framework for Identifying Mis-Localized Proteins across Pan-Cancer","publication_year":2025,"publication_date":"2025-12-23","ids":{"openalex":"https://openalex.org/W7117161823","doi":"https://doi.org/10.1021/acs.jcim.5c02226","pmid":"https://pubmed.ncbi.nlm.nih.gov/41436377"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c02226","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02226","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5121201062","display_name":"Bing Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I129708740","display_name":"Fujian Medical University","ror":"https://ror.org/050s6ns64","country_code":"CN","type":"education","lineage":["https://openalex.org/I129708740"]},{"id":"https://openalex.org/I3018851911","display_name":"Institute of Precision Mechanics","ror":"https://ror.org/02bxtrk46","country_code":"PL","type":"facility","lineage":["https://openalex.org/I3018851911"]}],"countries":["CN","PL"],"is_corresponding":false,"raw_author_name":"Bing Wang","raw_affiliation_strings":["Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Institute of Precision Medicine, School of Medical Technology and Engineering","Fujian Medical University","Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education"],"raw_orcid":"https://orcid.org/0000-0003-0684-2789","affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Institute of Precision Medicine, School of Medical Technology and Engineering","institution_ids":["https://openalex.org/I3018851911"]},{"raw_affiliation_string":"Fujian Medical University","institution_ids":["https://openalex.org/I129708740"]},{"raw_affiliation_string":"Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education","institution_ids":["https://openalex.org/I129708740"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5121210196","display_name":"Qilei Lin","orcid":null},"institutions":[{"id":"https://openalex.org/I129708740","display_name":"Fujian Medical University","ror":"https://ror.org/050s6ns64","country_code":"CN","type":"education","lineage":["https://openalex.org/I129708740"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qilei Lin","raw_affiliation_strings":["Fujian Medical University","School of Medical Imaging"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fujian Medical University","institution_ids":["https://openalex.org/I129708740"]},{"raw_affiliation_string":"School of Medical Imaging","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5121238271","display_name":"Xin He","orcid":null},"institutions":[{"id":"https://openalex.org/I4210120302","display_name":"Shunde Polytechnic","ror":"https://ror.org/01w9d4603","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210120302"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xin He","raw_affiliation_strings":["College of Intelligent Manufacturing","Foshan Polytechnic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Intelligent Manufacturing","institution_ids":[]},{"raw_affiliation_string":"Foshan Polytechnic","institution_ids":["https://openalex.org/I4210120302"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5121235819","display_name":"Shiyun Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I129708740","display_name":"Fujian Medical University","ror":"https://ror.org/050s6ns64","country_code":"CN","type":"education","lineage":["https://openalex.org/I129708740"]},{"id":"https://openalex.org/I3018851911","display_name":"Institute of Precision Mechanics","ror":"https://ror.org/02bxtrk46","country_code":"PL","type":"facility","lineage":["https://openalex.org/I3018851911"]}],"countries":["CN","PL"],"is_corresponding":false,"raw_author_name":"Shiyun Liu","raw_affiliation_strings":["Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Institute of Precision Medicine, School of Medical Technology and Engineering","Fujian Medical University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Institute of Precision Medicine, School of Medical Technology and Engineering","institution_ids":["https://openalex.org/I3018851911"]},{"raw_affiliation_string":"Fujian Medical University","institution_ids":["https://openalex.org/I129708740"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032882351","display_name":"Xiaopei Shen","orcid":"https://orcid.org/0000-0002-0004-4228"},"institutions":[{"id":"https://openalex.org/I129708740","display_name":"Fujian Medical University","ror":"https://ror.org/050s6ns64","country_code":"CN","type":"education","lineage":["https://openalex.org/I129708740"]},{"id":"https://openalex.org/I3018851911","display_name":"Institute of Precision Mechanics","ror":"https://ror.org/02bxtrk46","country_code":"PL","type":"facility","lineage":["https://openalex.org/I3018851911"]}],"countries":["CN","PL"],"is_corresponding":true,"raw_author_name":"Xiaopei Shen","raw_affiliation_strings":["Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Institute of Precision Medicine, School of Medical Technology and Engineering","Fujian Medical University","Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Institute of Precision Medicine, School of Medical Technology and Engineering","institution_ids":["https://openalex.org/I3018851911"]},{"raw_affiliation_string":"Fujian Medical University","institution_ids":["https://openalex.org/I129708740"]},{"raw_affiliation_string":"Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education","institution_ids":["https://openalex.org/I129708740"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5032882351"],"corresponding_institution_ids":["https://openalex.org/I129708740","https://openalex.org/I3018851911"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.54557464,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"66","issue":"1","first_page":"756","last_page":"769"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.43050000071525574,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.43050000071525574,"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":0.40369999408721924,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.06300000101327896,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.6841999888420105},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.5697000026702881},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.45419999957084656},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.399399995803833},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.3587999939918518},{"id":"https://openalex.org/keywords/protein-interaction-networks","display_name":"Protein Interaction Networks","score":0.35280001163482666},{"id":"https://openalex.org/keywords/relevance","display_name":"Relevance (law)","score":0.35199999809265137},{"id":"https://openalex.org/keywords/posttranslational-modification","display_name":"Posttranslational modification","score":0.3472999930381775}],"concepts":[{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.6841999888420105},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6093000173568726},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5860000252723694},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.5697000026702881},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5367000102996826},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5184999704360962},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.45419999957084656},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.399399995803833},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.3587999939918518},{"id":"https://openalex.org/C2909613950","wikidata":"https://www.wikidata.org/wiki/Q158695","display_name":"Protein Interaction Networks","level":3,"score":0.35280001163482666},{"id":"https://openalex.org/C158154518","wikidata":"https://www.wikidata.org/wiki/Q7310970","display_name":"Relevance (law)","level":2,"score":0.35199999809265137},{"id":"https://openalex.org/C100631289","wikidata":"https://www.wikidata.org/wiki/Q898362","display_name":"Posttranslational modification","level":3,"score":0.3472999930381775},{"id":"https://openalex.org/C2776879804","wikidata":"https://www.wikidata.org/wiki/Q7630919","display_name":"Subcellular localization","level":3,"score":0.33629998564720154},{"id":"https://openalex.org/C80311884","wikidata":"https://www.wikidata.org/wiki/Q7268939","display_name":"Quantitative proteomics","level":4,"score":0.30889999866485596},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.2962000072002411},{"id":"https://openalex.org/C45942800","wikidata":"https://www.wikidata.org/wiki/Q245652","display_name":"Ensemble learning","level":2,"score":0.29510000348091125},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.29019999504089355},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.2797999978065491},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2773999869823456},{"id":"https://openalex.org/C151201525","wikidata":"https://www.wikidata.org/wiki/Q177239","display_name":"Limit (mathematics)","level":2,"score":0.2759999930858612},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.2556000053882599}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5c02226","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02226","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:41436377","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41436377","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3819548204","display_name":null,"funder_award_id":"XRCZX2024018","funder_id":"https://openalex.org/F4320328113","funder_display_name":"Fujian Medical University"},{"id":"https://openalex.org/G4068378612","display_name":"\u57fa\u4e8e\u5355\u7ec6\u80de\u6fc0\u9176\u6d3b\u6027\u63a8\u65ad\u7684\u836f\u7269\u91cd\u5b9a\u4f4d\u7814\u7a76","funder_award_id":"2025J01842","funder_id":"https://openalex.org/F4320321878","funder_display_name":"Natural Science Foundation of Fujian Province"},{"id":"https://openalex.org/G5608768533","display_name":null,"funder_award_id":"2023J01321","funder_id":"https://openalex.org/F4320321878","funder_display_name":"Natural Science Foundation of Fujian Province"}],"funders":[{"id":"https://openalex.org/F4320321878","display_name":"Natural Science Foundation of Fujian Province","ror":null},{"id":"https://openalex.org/F4320328113","display_name":"Fujian Medical University","ror":"https://ror.org/050s6ns64"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W1990955264","https://openalex.org/W2041522424","https://openalex.org/W2049497130","https://openalex.org/W2050052936","https://openalex.org/W2069547574","https://openalex.org/W2070923004","https://openalex.org/W2092485963","https://openalex.org/W2101520349","https://openalex.org/W2108984616","https://openalex.org/W2132946679","https://openalex.org/W2152482858","https://openalex.org/W2154459622","https://openalex.org/W2159707944","https://openalex.org/W2172854830","https://openalex.org/W2340761255","https://openalex.org/W2587745846","https://openalex.org/W2799284926","https://openalex.org/W2945220204","https://openalex.org/W2996617366","https://openalex.org/W3038061184","https://openalex.org/W3093053585","https://openalex.org/W3093641852","https://openalex.org/W3094031749","https://openalex.org/W3124088661","https://openalex.org/W3180836662","https://openalex.org/W4200263582","https://openalex.org/W4213337194","https://openalex.org/W4225291593","https://openalex.org/W4282926909","https://openalex.org/W4293275695","https://openalex.org/W4303982961","https://openalex.org/W4307908388","https://openalex.org/W4309944312","https://openalex.org/W4319812277","https://openalex.org/W4323830612","https://openalex.org/W4362459376","https://openalex.org/W4379390412","https://openalex.org/W4380182220","https://openalex.org/W4380536315","https://openalex.org/W4385796046","https://openalex.org/W4386117213","https://openalex.org/W4392393062","https://openalex.org/W4394619651","https://openalex.org/W4394718159","https://openalex.org/W4398171969","https://openalex.org/W4403479110","https://openalex.org/W4406781476","https://openalex.org/W4406917397","https://openalex.org/W4408541231"],"related_works":[],"abstract_inverted_index":{"Accurate":[0],"protein":[1,15,79,147],"subcellular":[2],"localization":[3],"(PSL)":[4],"is":[5],"essential":[6],"for":[7,122],"proteins":[8,49],"to":[9,23,104],"perform":[10],"their":[11,38,156,166],"biological":[12,168],"functions,":[13],"whereas":[14],"mis-localization":[16],"can":[17],"disrupt":[18],"cellular":[19],"processes":[20],"and":[21,41,120,127,139,162],"contribute":[22],"various":[24],"diseases,":[25],"particularly":[26],"cancer.":[27,52],"Although":[28],"spatial":[29],"proteomics":[30,74],"technologies":[31],"have":[32],"enabled":[33],"systematic":[34],"studies":[35],"of":[36,47,144,152],"PSL,":[37],"high":[39],"cost":[40],"technical":[42],"complexity":[43],"limit":[44],"large-scale":[45,71],"analysis":[46],"mis-localized":[48,146],"(MLPs)":[50],"in":[51,117,125,159,170],"To":[53],"address":[54],"this":[55],"challenge,":[56],"we":[57,131],"propose":[58],"DeepMLP,":[59],"a":[60,82,142],"proteomics-driven":[61],"deep":[62],"learning":[63],"framework":[64],"that":[65,111],"identifies":[66],"MLPs":[67,135,154],"across":[68,136],"cancers":[69],"using":[70],"mass":[72],"spectrometry-based":[73],"data.":[75],"It":[76],"constructs":[77],"pathway-aware":[78],"representations":[80,89],"via":[81],"cross-attention":[83],"mechanism":[84],"and,":[85],"by":[86],"integrating":[87],"these":[88,153],"with":[90],"dynamic":[91],"protein-protein":[92],"interaction":[93],"(PPI)":[94],"networks":[95],"through":[96],"graph":[97],"attention":[98],"networks,":[99],"synergistically":[100],"enhances":[101],"the":[102],"ability":[103],"uncover":[105],"potential":[106,134,145,167],"cancer":[107],"MLPs.":[108],"Benchmarking":[109],"demonstrated":[110],"DeepMLP":[112],"consistently":[113],"outperformed":[114],"state-of-the-art":[115],"methods":[116],"both":[118],"accuracy":[119],"stability":[121],"PSL":[123],"prediction":[124],"normal":[126],"tumor":[128],"conditions.":[129],"Furthermore,":[130],"systematically":[132],"identified":[133],"pan-cancer":[137],"types":[138],"further":[140],"uncovered":[141],"subset":[143],"kinases.":[148],"Functional":[149],"enrichment":[150],"analyses":[151],"revealed":[155],"significant":[157],"involvement":[158],"cancer-related":[160],"metabolic":[161],"signaling":[163],"pathways,":[164],"highlighting":[165],"relevance":[169],"tumorigenesis.":[171]},"counts_by_year":[],"updated_date":"2026-07-13T07:31:44.756512","created_date":"2025-12-24T00:00:00"}