{"id":"https://openalex.org/W4409278154","doi":"https://doi.org/10.1093/bib/bbaf143","title":"Inferring kinase\u2013phosphosite regulation from phosphoproteome-enriched cancer multi-omics datasets","display_name":"Inferring kinase\u2013phosphosite regulation from phosphoproteome-enriched cancer multi-omics datasets","publication_year":2025,"publication_date":"2025-03-01","ids":{"openalex":"https://openalex.org/W4409278154","doi":"https://doi.org/10.1093/bib/bbaf143","pmid":"https://pubmed.ncbi.nlm.nih.gov/40194556"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf143","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf143","pdf_url":"https://academic.oup.com/bib/article-pdf/26/2/bbaf143/62885689/bbaf143.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in 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/bib/article-pdf/26/2/bbaf143/62885689/bbaf143.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070490953","display_name":"H Cheng","orcid":null},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]},{"id":"https://openalex.org/I38877650","display_name":"Zhengzhou University","ror":"https://ror.org/04ypx8c21","country_code":"CN","type":"education","lineage":["https://openalex.org/I38877650"]},{"id":"https://openalex.org/I4210146711","display_name":"Sun Yat-sen University Cancer Center","ror":"https://ror.org/0400g8r85","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210146711"]},{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["CN","HK"],"is_corresponding":false,"raw_author_name":"Haoyang Cheng","raw_affiliation_strings":["Department of Computer Science, The University of Hong Kong , Pokfulam Road, Hong Kong Special Administrative Region 999077,","School of Life Sciences, Zhengzhou University , 100 Science Avenue, Zhengzhou 450001 ,","State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center , 651 Dongfeng East Road, Guangzhou 510060 ,"],"raw_orcid":"https://orcid.org/0009-0000-4692-619X","affiliations":[{"raw_affiliation_string":"Department of Computer Science, The University of Hong Kong , Pokfulam Road, Hong Kong Special Administrative Region 999077,","institution_ids":["https://openalex.org/I889458895"]},{"raw_affiliation_string":"School of Life Sciences, Zhengzhou University , 100 Science Avenue, Zhengzhou 450001 ,","institution_ids":["https://openalex.org/I38877650"]},{"raw_affiliation_string":"State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center , 651 Dongfeng East Road, Guangzhou 510060 ,","institution_ids":["https://openalex.org/I157773358","https://openalex.org/I4210146711"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022761412","display_name":"Zhuoran Liang","orcid":null},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]},{"id":"https://openalex.org/I4210146711","display_name":"Sun Yat-sen University Cancer Center","ror":"https://ror.org/0400g8r85","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210146711"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhuoran Liang","raw_affiliation_strings":["State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center , 651 Dongfeng East Road, Guangzhou 510060 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center , 651 Dongfeng East Road, Guangzhou 510060 ,","institution_ids":["https://openalex.org/I157773358","https://openalex.org/I4210146711"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016437579","display_name":"Yijin Wu","orcid":"https://orcid.org/0000-0002-6169-9084"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]},{"id":"https://openalex.org/I4210146711","display_name":"Sun Yat-sen University Cancer Center","ror":"https://ror.org/0400g8r85","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210146711"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yijin Wu","raw_affiliation_strings":["State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center , 651 Dongfeng East Road, Guangzhou 510060 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center , 651 Dongfeng East Road, Guangzhou 510060 ,","institution_ids":["https://openalex.org/I157773358","https://openalex.org/I4210146711"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101920826","display_name":"Jiamin Hu","orcid":"https://orcid.org/0000-0002-1413-5737"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]},{"id":"https://openalex.org/I4210146711","display_name":"Sun Yat-sen University Cancer Center","ror":"https://ror.org/0400g8r85","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210146711"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiamin Hu","raw_affiliation_strings":["State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center , 651 Dongfeng East Road, Guangzhou 510060 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center , 651 Dongfeng East Road, Guangzhou 510060 ,","institution_ids":["https://openalex.org/I157773358","https://openalex.org/I4210146711"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073981351","display_name":"Bijin Cao","orcid":null},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]},{"id":"https://openalex.org/I38877650","display_name":"Zhengzhou University","ror":"https://ror.org/04ypx8c21","country_code":"CN","type":"education","lineage":["https://openalex.org/I38877650"]},{"id":"https://openalex.org/I4210146711","display_name":"Sun Yat-sen University Cancer Center","ror":"https://ror.org/0400g8r85","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210146711"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bijin Cao","raw_affiliation_strings":["School of Life Sciences, Zhengzhou University , 100 Science Avenue, Zhengzhou 450001 ,","State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center , 651 Dongfeng East Road, Guangzhou 510060 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Life Sciences, Zhengzhou University , 100 Science Avenue, Zhengzhou 450001 ,","institution_ids":["https://openalex.org/I38877650"]},{"raw_affiliation_string":"State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center , 651 Dongfeng East Road, Guangzhou 510060 ,","institution_ids":["https://openalex.org/I157773358","https://openalex.org/I4210146711"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113426106","display_name":"Zekun Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]},{"id":"https://openalex.org/I4210146711","display_name":"Sun Yat-sen University Cancer Center","ror":"https://ror.org/0400g8r85","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210146711"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zekun Liu","raw_affiliation_strings":["State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center , 651 Dongfeng East Road, Guangzhou 510060 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center , 651 Dongfeng East Road, Guangzhou 510060 ,","institution_ids":["https://openalex.org/I157773358","https://openalex.org/I4210146711"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100461663","display_name":"Bo Liu","orcid":"https://orcid.org/0000-0002-5375-0505"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]},{"id":"https://openalex.org/I38877650","display_name":"Zhengzhou University","ror":"https://ror.org/04ypx8c21","country_code":"CN","type":"education","lineage":["https://openalex.org/I38877650"]},{"id":"https://openalex.org/I4210146711","display_name":"Sun Yat-sen University Cancer Center","ror":"https://ror.org/0400g8r85","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210146711"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bo Liu","raw_affiliation_strings":["School of Life Sciences, Zhengzhou University , 100 Science Avenue, Zhengzhou 450001 ,","State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center , 651 Dongfeng East Road, Guangzhou 510060 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Life Sciences, Zhengzhou University , 100 Science Avenue, Zhengzhou 450001 ,","institution_ids":["https://openalex.org/I38877650"]},{"raw_affiliation_string":"State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center , 651 Dongfeng East Road, Guangzhou 510060 ,","institution_ids":["https://openalex.org/I157773358","https://openalex.org/I4210146711"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083819240","display_name":"Han Cheng","orcid":"https://orcid.org/0000-0002-6684-317X"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]},{"id":"https://openalex.org/I38877650","display_name":"Zhengzhou University","ror":"https://ror.org/04ypx8c21","country_code":"CN","type":"education","lineage":["https://openalex.org/I38877650"]},{"id":"https://openalex.org/I4210146711","display_name":"Sun Yat-sen University Cancer Center","ror":"https://ror.org/0400g8r85","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210146711"]},{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["CN","HK"],"is_corresponding":false,"raw_author_name":"Han Cheng","raw_affiliation_strings":["Department of Computer Science, The University of Hong Kong , Pokfulam Road, Hong Kong Special Administrative Region 999077,","School of Life Sciences, Zhengzhou University , 100 Science Avenue, Zhengzhou 450001 ,","State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center , 651 Dongfeng East Road, Guangzhou 510060 ,"],"raw_orcid":"https://orcid.org/0000-0002-6684-317X","affiliations":[{"raw_affiliation_string":"Department of Computer Science, The University of Hong Kong , Pokfulam Road, Hong Kong Special Administrative Region 999077,","institution_ids":["https://openalex.org/I889458895"]},{"raw_affiliation_string":"School of Life Sciences, Zhengzhou University , 100 Science Avenue, Zhengzhou 450001 ,","institution_ids":["https://openalex.org/I38877650"]},{"raw_affiliation_string":"State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center , 651 Dongfeng East Road, Guangzhou 510060 ,","institution_ids":["https://openalex.org/I157773358","https://openalex.org/I4210146711"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027890976","display_name":"Zexian Liu","orcid":"https://orcid.org/0000-0001-9698-0610"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]},{"id":"https://openalex.org/I4210146711","display_name":"Sun Yat-sen University Cancer Center","ror":"https://ror.org/0400g8r85","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210146711"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ze-Xian Liu","raw_affiliation_strings":["State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center , 651 Dongfeng East Road, Guangzhou 510060 ,"],"raw_orcid":"https://orcid.org/0000-0001-9698-0610","affiliations":[{"raw_affiliation_string":"State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center , 651 Dongfeng East Road, Guangzhou 510060 ,","institution_ids":["https://openalex.org/I157773358","https://openalex.org/I4210146711"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.4868,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.61363276,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"26","issue":"2","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":0.9998999834060669,"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":0.9998999834060669,"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":0.9980999827384949,"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":0.9937000274658203,"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/phosphorylation","display_name":"Phosphorylation","score":0.6919549107551575},{"id":"https://openalex.org/keywords/kinase","display_name":"Kinase","score":0.6539967060089111},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5485745668411255},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5232136249542236},{"id":"https://openalex.org/keywords/oversampling","display_name":"Oversampling","score":0.44096219539642334},{"id":"https://openalex.org/keywords/protein-phosphorylation","display_name":"Protein phosphorylation","score":0.41425955295562744},{"id":"https://openalex.org/keywords/protein-kinase-a","display_name":"Protein kinase A","score":0.37496232986450195},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3291233777999878},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.31180816888809204},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.29803887009620667}],"concepts":[{"id":"https://openalex.org/C11960822","wikidata":"https://www.wikidata.org/wiki/Q242736","display_name":"Phosphorylation","level":2,"score":0.6919549107551575},{"id":"https://openalex.org/C184235292","wikidata":"https://www.wikidata.org/wiki/Q421851","display_name":"Kinase","level":2,"score":0.6539967060089111},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5485745668411255},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5232136249542236},{"id":"https://openalex.org/C197323446","wikidata":"https://www.wikidata.org/wiki/Q331222","display_name":"Oversampling","level":3,"score":0.44096219539642334},{"id":"https://openalex.org/C87325107","wikidata":"https://www.wikidata.org/wiki/Q7251493","display_name":"Protein phosphorylation","level":4,"score":0.41425955295562744},{"id":"https://openalex.org/C97029542","wikidata":"https://www.wikidata.org/wiki/Q281417","display_name":"Protein kinase A","level":3,"score":0.37496232986450195},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3291233777999878},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.31180816888809204},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.29803887009620667},{"id":"https://openalex.org/C2776257435","wikidata":"https://www.wikidata.org/wiki/Q1576430","display_name":"Bandwidth (computing)","level":2,"score":0.0},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"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":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010750","descriptor_name":"Phosphoproteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010750","descriptor_name":"Phosphoproteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010750","descriptor_name":"Phosphoproteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010750","descriptor_name":"Phosphoproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010750","descriptor_name":"Phosphoproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010750","descriptor_name":"Phosphoproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010770","descriptor_name":"Phosphotransferases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010770","descriptor_name":"Phosphotransferases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010770","descriptor_name":"Phosphotransferases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011494","descriptor_name":"Protein Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011494","descriptor_name":"Protein Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011494","descriptor_name":"Protein Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf143","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf143","pdf_url":"https://academic.oup.com/bib/article-pdf/26/2/bbaf143/62885689/bbaf143.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40194556","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40194556","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:10787908","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11975364","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf143","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf143","pdf_url":"https://academic.oup.com/bib/article-pdf/26/2/bbaf143/62885689/bbaf143.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1719194037","display_name":null,"funder_award_id":"2021YFA1302100","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G3183247085","display_name":null,"funder_award_id":"2021YFA1302100","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4118779827","display_name":null,"funder_award_id":"32370698","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4207602180","display_name":null,"funder_award_id":"91953123","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321160","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320336632","display_name":"Sun Yat-sen University Cancer Center","ror":"https://ror.org/0400g8r85"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4409278154.pdf","grobid_xml":"https://content.openalex.org/works/W4409278154.grobid-xml"},"referenced_works_count":91,"referenced_works":["https://openalex.org/W1482869707","https://openalex.org/W1516333482","https://openalex.org/W1608710587","https://openalex.org/W1886963552","https://openalex.org/W1964504843","https://openalex.org/W1995989434","https://openalex.org/W2013686278","https://openalex.org/W2019334044","https://openalex.org/W2028387937","https://openalex.org/W2031028006","https://openalex.org/W2035817829","https://openalex.org/W2043274355","https://openalex.org/W2047006637","https://openalex.org/W2057272791","https://openalex.org/W2085037886","https://openalex.org/W2092099098","https://openalex.org/W2093509030","https://openalex.org/W2099686283","https://openalex.org/W2109021234","https://openalex.org/W2109509105","https://openalex.org/W2122863289","https://openalex.org/W2148143831","https://openalex.org/W2158266834","https://openalex.org/W2162172965","https://openalex.org/W2171649066","https://openalex.org/W2306215265","https://openalex.org/W2442313203","https://openalex.org/W2464880876","https://openalex.org/W2560075025","https://openalex.org/W2563500611","https://openalex.org/W2635415917","https://openalex.org/W2742750032","https://openalex.org/W2767377392","https://openalex.org/W2793783646","https://openalex.org/W2794930605","https://openalex.org/W2891014905","https://openalex.org/W2909516037","https://openalex.org/W2912820434","https://openalex.org/W2918023653","https://openalex.org/W2940627982","https://openalex.org/W2967976704","https://openalex.org/W2977528366","https://openalex.org/W2982402173","https://openalex.org/W2985457336","https://openalex.org/W3005970532","https://openalex.org/W3006211741","https://openalex.org/W3007726005","https://openalex.org/W3011725683","https://openalex.org/W3041116333","https://openalex.org/W3041219630","https://openalex.org/W3041397352","https://openalex.org/W3081768459","https://openalex.org/W3082931165","https://openalex.org/W3091403740","https://openalex.org/W3095644091","https://openalex.org/W3096333766","https://openalex.org/W3104755560","https://openalex.org/W3108158555","https://openalex.org/W3119681293","https://openalex.org/W3120294717","https://openalex.org/W3126609356","https://openalex.org/W3176077722","https://openalex.org/W3188077199","https://openalex.org/W3196572132","https://openalex.org/W3199725740","https://openalex.org/W3205283328","https://openalex.org/W3207731098","https://openalex.org/W3212237028","https://openalex.org/W3214112664","https://openalex.org/W4200501239","https://openalex.org/W4206956476","https://openalex.org/W4210871270","https://openalex.org/W4226059287","https://openalex.org/W4229033126","https://openalex.org/W4283754853","https://openalex.org/W4292953230","https://openalex.org/W4297237740","https://openalex.org/W4311549355","https://openalex.org/W4315642941","https://openalex.org/W4315645662","https://openalex.org/W4317241289","https://openalex.org/W4318930189","https://openalex.org/W4323812728","https://openalex.org/W4379016122","https://openalex.org/W4380576406","https://openalex.org/W4384500119","https://openalex.org/W4385230052","https://openalex.org/W4385796046","https://openalex.org/W4386101529","https://openalex.org/W4387767260","https://openalex.org/W4391075295"],"related_works":["https://openalex.org/W2051108283","https://openalex.org/W2352214813","https://openalex.org/W1964515703","https://openalex.org/W2491608603","https://openalex.org/W941583161","https://openalex.org/W2505862120","https://openalex.org/W1576619789","https://openalex.org/W4223412920","https://openalex.org/W1973530967","https://openalex.org/W4362623556"],"abstract_inverted_index":{"Phosphorylation":[0],"in":[1,8,23,86,105,145,156,193],"eukaryotic":[2],"cells":[3],"plays":[4],"a":[5,24,110,126],"key":[6],"role":[7],"regulating":[9,34],"cell":[10],"signaling":[11],"and":[12,52,63,77,88,99,117,183,199,219,229],"disease":[13],"progression.":[14],"Despite":[15],"the":[16,30,45,49,74,118,131,135,161,196,207,224],"ability":[17],"to":[18,72,187],"detect":[19],"thousands":[20],"of":[21,55,79,121,164,201],"phosphosites":[22],"single":[25],"experiment":[26],"using":[27],"high-throughput":[28],"technologies,":[29],"kinases":[31,228],"responsible":[32],"for":[33,139],"these":[35,140,150],"sites":[36,192],"are":[37,153],"largely":[38],"unidentified.":[39],"To":[40],"solve":[41],"this,":[42],"we":[43,170],"collected":[44],"quantitative":[46,127],"data":[47],"at":[48],"transcriptional,":[50],"protein,":[51],"phosphorylation":[53,119,191],"levels":[54],"10":[56],"159":[57],"samples":[58],"from":[59],"23":[60],"tumor":[61,146],"datasets":[62,166],"15":[64],"adjacent":[65],"normal":[66],"tissue":[67],"datasets.":[68],"Our":[69],"analysis":[70],"aimed":[71],"uncover":[73],"potential":[75,189],"impact":[76],"linkage":[78],"kinase-phosphosite":[80,202],"(KPS)":[81],"pairs":[82,102,141],"through":[83],"experimental":[84],"evidence":[85],"publications":[87],"prediction":[89],"tools":[90],"commonly":[91],"used.":[92],"We":[93],"discovered":[94],"that":[95,125,149,176],"both":[96],"experimentally":[97],"validated":[98],"tool-predicted":[100],"KPS":[101,132,162],"were":[103,142,204],"enriched":[104],"groups":[106],"where":[107],"there":[108],"is":[109],"significant":[111],"correlation":[112,128,137],"between":[113,227],"kinase":[114],"expression/phosphorylation":[115],"level":[116,120],"phosphosite.":[122],"This":[123],"suggested":[124],"could":[129,215],"infer":[130],"interconnections.":[133],"Furthermore,":[134],"Spearman's":[136],"coefficient":[138],"notably":[143],"higher":[144],"samples,":[147],"indicating":[148],"regulatory":[151,225],"interactions":[152],"particularly":[154],"pronounced":[155],"tumors.":[157],"Consequently,":[158],"building":[159],"on":[160,223],"correlations":[163,198],"different":[165],"as":[167],"predictive":[168],"features,":[169],"have":[171],"developed":[172],"an":[173,178],"innovative":[174],"approach":[175],"employed":[177],"oversampling":[179],"method":[180],"combined":[181],"with":[182],"XGBoost":[184],"algorithm":[185],"(SMOTE-XGBoost)":[186],"predict":[188],"kinase-specific":[190],"proteins.":[194],"Moreover,":[195],"computed":[197],"predictions":[200],"interconnections":[203],"integrated":[205],"into":[206],"eKPI":[208],"database":[209],"(https://ekpi.omicsbio.info/).":[210],"In":[211],"summary,":[212],"our":[213],"study":[214],"provide":[216],"helpful":[217],"information":[218],"facilitate":[220],"further":[221],"research":[222],"relationship":[226],"phosphosites.":[230]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
