{"id":"https://openalex.org/W4361255792","doi":"https://doi.org/10.1371/journal.pcbi.1010690","title":"Network models of protein phosphorylation, acetylation, and ubiquitination connect metabolic and cell signaling pathways in lung cancer","display_name":"Network models of protein phosphorylation, acetylation, and ubiquitination connect metabolic and cell signaling pathways in lung cancer","publication_year":2023,"publication_date":"2023-03-30","ids":{"openalex":"https://openalex.org/W4361255792","doi":"https://doi.org/10.1371/journal.pcbi.1010690","pmid":"https://pubmed.ncbi.nlm.nih.gov/36996232"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1010690","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010690","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010690&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010690&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010355751","display_name":"Karen Ross","orcid":"https://orcid.org/0000-0003-4633-6055"},"institutions":[{"id":"https://openalex.org/I2799903593","display_name":"Georgetown University Medical Center","ror":"https://ror.org/00hjz7x27","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799903593"]},{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Karen E. Ross","raw_affiliation_strings":["Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, United States of America","institution_ids":["https://openalex.org/I2799903593","https://openalex.org/I184565670"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084573973","display_name":"Guolin Zhang","orcid":"https://orcid.org/0000-0002-7603-1933"},"institutions":[{"id":"https://openalex.org/I3019308854","display_name":"Moffitt Cancer Center","ror":"https://ror.org/01xf75524","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I3019308854"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Guolin Zhang","raw_affiliation_strings":["Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America","institution_ids":["https://openalex.org/I3019308854"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045418504","display_name":"C\u00fcneyt G\u00fcrcan Ak\u00e7ora","orcid":"https://orcid.org/0000-0002-2882-6950"},"institutions":[{"id":"https://openalex.org/I46247651","display_name":"University of Manitoba","ror":"https://ror.org/02gfys938","country_code":"CA","type":"education","lineage":["https://openalex.org/I46247651"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Cuneyt Akcora","raw_affiliation_strings":["Department of Computer Science and Statistics, University of Manitoba, Winnipeg, Manitoba Canada"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Statistics, University of Manitoba, Winnipeg, Manitoba Canada","institution_ids":["https://openalex.org/I46247651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110966497","display_name":"Yu Lin","orcid":null},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]},{"id":"https://openalex.org/I2799903593","display_name":"Georgetown University Medical Center","ror":"https://ror.org/00hjz7x27","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799903593"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yu Lin","raw_affiliation_strings":["Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, United States of America","institution_ids":["https://openalex.org/I2799903593","https://openalex.org/I184565670"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076672524","display_name":"Bin Fang","orcid":"https://orcid.org/0000-0002-7636-1318"},"institutions":[{"id":"https://openalex.org/I3019308854","display_name":"Moffitt Cancer Center","ror":"https://ror.org/01xf75524","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I3019308854"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bin Fang","raw_affiliation_strings":["Proteomics & Metabolomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America"],"affiliations":[{"raw_affiliation_string":"Proteomics & Metabolomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America","institution_ids":["https://openalex.org/I3019308854"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002876951","display_name":"John M. Koomen","orcid":"https://orcid.org/0000-0002-3818-1762"},"institutions":[{"id":"https://openalex.org/I4210150208","display_name":"Molecular Oncology (United States)","ror":"https://ror.org/04rtkc841","country_code":"US","type":"company","lineage":["https://openalex.org/I4210150208"]},{"id":"https://openalex.org/I3019308854","display_name":"Moffitt Cancer Center","ror":"https://ror.org/01xf75524","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I3019308854"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"John Koomen","raw_affiliation_strings":["Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America"],"affiliations":[{"raw_affiliation_string":"Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America","institution_ids":["https://openalex.org/I3019308854","https://openalex.org/I4210150208"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064494204","display_name":"Eric B. Haura","orcid":"https://orcid.org/0000-0003-3114-1909"},"institutions":[{"id":"https://openalex.org/I3019308854","display_name":"Moffitt Cancer Center","ror":"https://ror.org/01xf75524","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I3019308854"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Eric B. Haura","raw_affiliation_strings":["Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America","institution_ids":["https://openalex.org/I3019308854"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010668546","display_name":"Mark L. Grimes","orcid":"https://orcid.org/0000-0003-2673-5892"},"institutions":[{"id":"https://openalex.org/I6750721","display_name":"University of Montana","ror":"https://ror.org/0078xmk34","country_code":"US","type":"education","lineage":["https://openalex.org/I6750721"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mark Grimes","raw_affiliation_strings":["Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America"],"affiliations":[{"raw_affiliation_string":"Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America","institution_ids":["https://openalex.org/I6750721"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5002876951","https://openalex.org/A5010355751","https://openalex.org/A5010668546","https://openalex.org/A5045418504","https://openalex.org/A5064494204","https://openalex.org/A5076672524","https://openalex.org/A5084573973","https://openalex.org/A5110966497"],"corresponding_institution_ids":["https://openalex.org/I184565670","https://openalex.org/I2799903593","https://openalex.org/I3019308854","https://openalex.org/I4210150208","https://openalex.org/I46247651","https://openalex.org/I6750721"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.509,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.89204733,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"19","issue":"3","first_page":"e1010690","last_page":"e1010690"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9997000098228455,"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":0.9997000098228455,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9966999888420105,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9958999752998352,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/crosstalk","display_name":"Crosstalk","score":0.6714745163917542},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6570494771003723},{"id":"https://openalex.org/keywords/signal-transduction","display_name":"Signal transduction","score":0.6326432824134827},{"id":"https://openalex.org/keywords/phosphoproteomics","display_name":"Phosphoproteomics","score":0.5788652896881104},{"id":"https://openalex.org/keywords/stable-isotope-labeling-by-amino-acids-in-cell-culture","display_name":"Stable isotope labeling by amino acids in cell culture","score":0.46929436922073364},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.46476539969444275},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.4449456036090851},{"id":"https://openalex.org/keywords/metabolic-pathway","display_name":"Metabolic pathway","score":0.43204209208488464},{"id":"https://openalex.org/keywords/phosphorylation","display_name":"Phosphorylation","score":0.35956114530563354},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.35585886240005493},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2954300045967102},{"id":"https://openalex.org/keywords/protein-phosphorylation","display_name":"Protein phosphorylation","score":0.27389559149742126},{"id":"https://openalex.org/keywords/protein-kinase-a","display_name":"Protein kinase A","score":0.2692630887031555}],"concepts":[{"id":"https://openalex.org/C169822122","wikidata":"https://www.wikidata.org/wiki/Q230187","display_name":"Crosstalk","level":2,"score":0.6714745163917542},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6570494771003723},{"id":"https://openalex.org/C62478195","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signal transduction","level":2,"score":0.6326432824134827},{"id":"https://openalex.org/C6675166","wikidata":"https://www.wikidata.org/wiki/Q7187538","display_name":"Phosphoproteomics","level":5,"score":0.5788652896881104},{"id":"https://openalex.org/C34905852","wikidata":"https://www.wikidata.org/wiki/Q3943646","display_name":"Stable isotope labeling by amino acids in cell culture","level":4,"score":0.46929436922073364},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.46476539969444275},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.4449456036090851},{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.43204209208488464},{"id":"https://openalex.org/C11960822","wikidata":"https://www.wikidata.org/wiki/Q242736","display_name":"Phosphorylation","level":2,"score":0.35956114530563354},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35585886240005493},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2954300045967102},{"id":"https://openalex.org/C87325107","wikidata":"https://www.wikidata.org/wiki/Q7251493","display_name":"Protein phosphorylation","level":4,"score":0.27389559149742126},{"id":"https://openalex.org/C97029542","wikidata":"https://www.wikidata.org/wiki/Q281417","display_name":"Protein kinase A","level":3,"score":0.2692630887031555},{"id":"https://openalex.org/C62231903","wikidata":"https://www.wikidata.org/wiki/Q1057","display_name":"Metabolism","level":2,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000107","descriptor_name":"Acetylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000107","descriptor_name":"Acetylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000107","descriptor_name":"Acetylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000107","descriptor_name":"Acetylation","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008239","descriptor_name":"Lysine","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008239","descriptor_name":"Lysine","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008239","descriptor_name":"Lysine","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008239","descriptor_name":"Lysine","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":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054875","descriptor_name":"Ubiquitination","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054875","descriptor_name":"Ubiquitination","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054875","descriptor_name":"Ubiquitination","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054875","descriptor_name":"Ubiquitination","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1010690","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010690","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010690&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:36996232","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36996232","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10089347","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10089347","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10089347/pdf/pcbi.1010690.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:92f7c2e322a64533a13b1a50cb4a282b","is_oa":true,"landing_page_url":"https://doaj.org/article/92f7c2e322a64533a13b1a50cb4a282b","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 19, Iss 3, p e1010690 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1010690","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010690","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010690&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.7900000214576721,"display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G1931346518","display_name":null,"funder_award_id":"P30-CA076292","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G2529056698","display_name":null,"funder_award_id":"R35GM141873","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G363453825","display_name":null,"funder_award_id":"partial","funder_id":"https://openalex.org/F4320307115","funder_display_name":"Bristol-Myers Squibb"},{"id":"https://openalex.org/G4066947090","display_name":null,"funder_award_id":"Moffitt Innovative Core Project","funder_id":"https://openalex.org/F4320308574","funder_display_name":"H. Lee Moffitt Cancer Center and Research Institute"},{"id":"https://openalex.org/G4551976579","display_name":null,"funder_award_id":"CA076292","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G6958627566","display_name":null,"funder_award_id":"P30-CA076292","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7191188309","display_name":null,"funder_award_id":"P30-CA076292","funder_id":"https://openalex.org/F4320311073","funder_display_name":"Moffitt Cancer Center"},{"id":"https://openalex.org/G8135003176","display_name":null,"funder_award_id":"CA076292","funder_id":"https://openalex.org/F4320311073","funder_display_name":"Moffitt Cancer Center"},{"id":"https://openalex.org/G8292783287","display_name":null,"funder_award_id":"R15DE028434","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320307115","display_name":"Bristol-Myers Squibb","ror":"https://ror.org/00gtmwv55"},{"id":"https://openalex.org/F4320308574","display_name":"H. Lee Moffitt Cancer Center and Research Institute","ror":"https://ror.org/032db5x82"},{"id":"https://openalex.org/F4320310589","display_name":"University of Montana","ror":"https://ror.org/0078xmk34"},{"id":"https://openalex.org/F4320311073","display_name":"Moffitt Cancer Center","ror":"https://ror.org/01xf75524"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4361255792.pdf","grobid_xml":"https://content.openalex.org/works/W4361255792.grobid-xml"},"referenced_works_count":83,"referenced_works":["https://openalex.org/W25499092","https://openalex.org/W229097380","https://openalex.org/W318276992","https://openalex.org/W1270834676","https://openalex.org/W1567806153","https://openalex.org/W1611787727","https://openalex.org/W1875842236","https://openalex.org/W1974515407","https://openalex.org/W1991161134","https://openalex.org/W1993754619","https://openalex.org/W1994107958","https://openalex.org/W1996923837","https://openalex.org/W2013853442","https://openalex.org/W2021128108","https://openalex.org/W2032708781","https://openalex.org/W2044865804","https://openalex.org/W2049133325","https://openalex.org/W2051664537","https://openalex.org/W2056017011","https://openalex.org/W2067178867","https://openalex.org/W2074129822","https://openalex.org/W2079967238","https://openalex.org/W2080752012","https://openalex.org/W2092530852","https://openalex.org/W2101065953","https://openalex.org/W2118439154","https://openalex.org/W2141112224","https://openalex.org/W2148606255","https://openalex.org/W2157421521","https://openalex.org/W2157658519","https://openalex.org/W2160697532","https://openalex.org/W2162318322","https://openalex.org/W2164298117","https://openalex.org/W2166542841","https://openalex.org/W2170532460","https://openalex.org/W2266484479","https://openalex.org/W2319361213","https://openalex.org/W2338466067","https://openalex.org/W2345356016","https://openalex.org/W2399911911","https://openalex.org/W2527715458","https://openalex.org/W2530450137","https://openalex.org/W2537623931","https://openalex.org/W2557253070","https://openalex.org/W2602011586","https://openalex.org/W2606595919","https://openalex.org/W2766431227","https://openalex.org/W2769423727","https://openalex.org/W2793487084","https://openalex.org/W2801699880","https://openalex.org/W2804894235","https://openalex.org/W2808551187","https://openalex.org/W2896871572","https://openalex.org/W2904323618","https://openalex.org/W2940964825","https://openalex.org/W2952254903","https://openalex.org/W2979407281","https://openalex.org/W2980543550","https://openalex.org/W2990609790","https://openalex.org/W3008105021","https://openalex.org/W3044145717","https://openalex.org/W3045609965","https://openalex.org/W3082755785","https://openalex.org/W3090855090","https://openalex.org/W3102922803","https://openalex.org/W3108630326","https://openalex.org/W3120888075","https://openalex.org/W3147142721","https://openalex.org/W3157357317","https://openalex.org/W3169413085","https://openalex.org/W3171164709","https://openalex.org/W3172174595","https://openalex.org/W3199257076","https://openalex.org/W3205875945","https://openalex.org/W4200051192","https://openalex.org/W4205614370","https://openalex.org/W4214832787","https://openalex.org/W4220780132","https://openalex.org/W4238928355","https://openalex.org/W4256503215","https://openalex.org/W6693524905","https://openalex.org/W6782346068","https://openalex.org/W6792798819"],"related_works":["https://openalex.org/W2792087494","https://openalex.org/W2057656847","https://openalex.org/W4309082212","https://openalex.org/W2103479321","https://openalex.org/W2257927092","https://openalex.org/W4210921807","https://openalex.org/W2060036358","https://openalex.org/W4288010073","https://openalex.org/W3159355857","https://openalex.org/W2621361731"],"abstract_inverted_index":{"We":[0,140],"analyzed":[1],"large-scale":[2],"post-translational":[3],"modification":[4,41],"(PTM)":[5],"data":[6,166],"to":[7,48,58,73,92,138,188],"outline":[8],"cell":[9,22,144,200],"signaling":[10,64,145,225],"pathways":[11,108,146,226],"affected":[12],"by":[13,106],"tyrosine":[14,175],"kinase":[15,176],"inhibitors":[16],"(TKIs)":[17],"in":[18,127,184],"ten":[19],"lung":[20,62,135,185,198],"cancer":[21,63,136,199],"lines.":[23],"Tyrosine":[24],"phosphorylated,":[25],"lysine":[26,29],"ubiquitinated,":[27],"and":[28,80,123,126,149,161,163,169,180,216,235],"acetylated":[30],"proteins":[31,114],"were":[32,71],"concomitantly":[33],"identified":[34],"using":[35],"sequential":[36],"enrichment":[37],"of":[38,89,134,158,197,206,220,222],"post":[39],"translational":[40],"(SEPTM)":[42],"proteomics.":[43],"Machine":[44],"learning":[45],"was":[46],"used":[47,72],"identify":[49,167],"PTM":[50,69],"clusters":[51,70],"that":[52,56,117],"represent":[53],"functional":[54],"modules":[55],"respond":[57],"TKIs.":[59,139],"To":[60],"model":[61],"at":[65],"the":[66,120,132],"protein":[67],"level,":[68],"create":[74,93],"a":[75,86,94,101,189,193,203],"co-cluster":[76],"correlation":[77],"network":[78,88,96],"(CCCN)":[79],"select":[81],"protein-protein":[82],"interactions":[83],"(PPIs)":[84],"from":[85,109,192],"large":[87],"curated":[90],"PPIs":[91,207],"cluster-filtered":[95],"(CFN).":[97],"Next,":[98],"we":[99],"constructed":[100],"Pathway":[102],"Crosstalk":[103],"Network":[104],"(PCN)":[105],"connecting":[107],"NCATS":[110],"BioPlanet":[111,154],"whose":[112],"member":[113],"have":[115],"PTMs":[116,229],"co-cluster.":[118],"Interrogating":[119],"CCCN,":[121],"CFN,":[122],"PCN":[124],"individually":[125],"combination":[128,241],"yields":[129],"insights":[130],"into":[131],"response":[133],"cells":[137],"highlight":[141],"examples":[142],"where":[143],"involving":[147,208],"EGFR":[148],"ALK":[150],"exhibit":[151],"crosstalk":[152,223],"with":[153],"pathways:":[155],"Transmembrane":[156],"transport":[157],"small":[159],"molecules;":[160],"Glycolysis":[162],"gluconeogenesis.":[164],"These":[165],"known":[168],"previously":[170],"unappreciated":[171],"connections":[172],"between":[173],"receptor":[174],"(RTK)":[177],"signal":[178],"transduction":[179],"oncogenic":[181],"metabolic":[182,212],"reprogramming":[183],"cancer.":[186],"Comparison":[187],"CFN":[190],"generated":[191],"previous":[194],"multi-PTM":[195],"analysis":[196],"lines":[201],"reveals":[202,230],"common":[204],"core":[205],"heat":[209],"shock/chaperone":[210],"proteins,":[211],"enzymes,":[213],"cytoskeletal":[214],"components,":[215],"RNA-binding":[217],"proteins.":[218],"Elucidation":[219],"points":[221],"among":[224],"employing":[227],"different":[228],"new":[231],"potential":[232],"drug":[233,242],"targets":[234],"candidates":[236],"for":[237],"synergistic":[238],"attack":[239],"through":[240],"therapy.":[243]},"counts_by_year":[{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":5}],"updated_date":"2026-03-16T09:10:04.655348","created_date":"2025-10-10T00:00:00"}