{"id":"https://openalex.org/W3208551392","doi":"https://doi.org/10.12688/f1000research.74395.1","title":"Leveraging biochemical reactions to unravel functional impacts of cancer somatic variants affecting protein interaction interfaces","display_name":"Leveraging biochemical reactions to unravel functional impacts of cancer somatic variants affecting protein interaction interfaces","publication_year":2021,"publication_date":"2021-11-03","ids":{"openalex":"https://openalex.org/W3208551392","doi":"https://doi.org/10.12688/f1000research.74395.1","mag":"3208551392","pmid":"https://pubmed.ncbi.nlm.nih.gov/36569594","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/9755755"},"language":"en","primary_location":{"id":"doi:10.12688/f1000research.74395.1","doi":"https://doi.org/10.12688/f1000research.74395.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.74395.1","pdf_url":"https://f1000research.com/articles/10-1111/v1/pdf","source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-70","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357","https://openalex.org/P4310320547"],"host_organization_lineage_names":["Faculty of 1000","Taylor & Francis"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"F1000Research","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://f1000research.com/articles/10-1111/v1/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069978192","display_name":"Francesco Raimondi","orcid":"https://orcid.org/0000-0002-6891-3178","observed_orcids":["https://orcid.org/0000-0002-6891-3178"]},"institutions":[{"id":"https://openalex.org/I157210198","display_name":"Scuola Normale Superiore","ror":"https://ror.org/03aydme10","country_code":"IT","type":"education","lineage":["https://openalex.org/I157210198"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Francesco Raimondi","raw_affiliation_strings":["BIO@SNS, Scuola Normale Superiore di Pisa, Pisa, Italy, Italy"],"raw_orcid":"https://orcid.org/0000-0002-6891-3178","affiliations":[{"raw_affiliation_string":"BIO@SNS, Scuola Normale Superiore di Pisa, Pisa, Italy, Italy","institution_ids":["https://openalex.org/I157210198"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075883686","display_name":"Joshua G. Burkhart","orcid":"https://orcid.org/0000-0001-9279-1556","observed_orcids":["https://orcid.org/0000-0001-9279-1556"]},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joshua G. Burkhart","raw_affiliation_strings":["Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, USA"],"raw_orcid":"https://orcid.org/0000-0001-9279-1556","affiliations":[{"raw_affiliation_string":"Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, USA","institution_ids":["https://openalex.org/I165690674"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040703948","display_name":"Matthew J. Betts","orcid":"https://orcid.org/0000-0003-4583-9814","observed_orcids":["https://orcid.org/0000-0003-4583-9814"]},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Matthew J. Betts","raw_affiliation_strings":["BioQuant, University of Heidelberg, Heidelberg, Germany","Heidelberg University Biochemistry Center, University of Heidelberg, Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioQuant, University of Heidelberg, Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909"]},{"raw_affiliation_string":"Heidelberg University Biochemistry Center, University of Heidelberg, Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108001959","display_name":"Robert B. Russell","orcid":"https://orcid.org/0000-0002-1905-4717","observed_orcids":["https://orcid.org/0000-0002-1905-4717"]},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Robert B. Russell","raw_affiliation_strings":["BioQuant, University of Heidelberg, Heidelberg, Germany","Heidelberg University Biochemistry Center, University of Heidelberg, Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioQuant, University of Heidelberg, Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909"]},{"raw_affiliation_string":"Heidelberg University Biochemistry Center, University of Heidelberg, Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006718188","display_name":"Guanming Wu","orcid":"https://orcid.org/0000-0001-8196-1177","observed_orcids":["https://orcid.org/0000-0001-8196-1177"]},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Guanming Wu","raw_affiliation_strings":["Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, USA"],"raw_orcid":"https://orcid.org/0000-0001-8196-1177","affiliations":[{"raw_affiliation_string":"Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, USA","institution_ids":["https://openalex.org/I165690674"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5006718188","https://openalex.org/A5069978192"],"corresponding_institution_ids":["https://openalex.org/I157210198","https://openalex.org/I165690674"],"apc_list":{"value":1350,"currency":"USD","value_usd":1350},"apc_paid":{"value":1350,"currency":"USD","value_usd":1350},"fwci":0.1568,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.38099728,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":93},"biblio":{"volume":"10","issue":null,"first_page":"1111","last_page":"1111"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9487000107765198,"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":0.9487000107765198,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.04259999841451645,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11642","display_name":"Genomics and Rare Diseases","score":0.003100000089034438,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/biochemical-reactions","display_name":"biochemical reactions","score":0.8069999814033508},{"id":"https://openalex.org/keywords/protein-protein-interfaces","display_name":"protein-protein interfaces","score":0.8669999837875366},{"id":"https://openalex.org/keywords/reactome","display_name":"Reactome","score":0.6380000114440918},{"id":"https://openalex.org/keywords/rare-mutations","display_name":"rare mutations","score":0.7400000095367432},{"id":"https://openalex.org/keywords/patient-stratification","display_name":"patient stratification","score":0.671999990940094},{"id":"https://openalex.org/keywords/survival-time","display_name":"survival time","score":0.7310000061988831},{"id":"https://openalex.org/keywords/g-protein-coupled-receptor-signaling","display_name":"G protein-coupled receptor signaling","score":0.8500000238418579},{"id":"https://openalex.org/keywords/pik3ca","display_name":"PIK3CA","score":0.8799999952316284},{"id":"https://openalex.org/keywords/complement-system","display_name":"complement system","score":0.8700000047683716},{"id":"https://openalex.org/keywords/personalized-medicine","display_name":"personalized medicine","score":0.4560000002384186},{"id":"https://openalex.org/keywords/the-cancer-genome-atlas","display_name":"TCGA","score":0.6629999876022339}],"concepts":[{"id":"https://openalex.org/C2983643791","wikidata":"https://www.wikidata.org/wiki/Q1999993","display_name":"Open peer review","level":3,"score":0.832236647605896},{"id":"https://openalex.org/C134305767","wikidata":"https://www.wikidata.org/wiki/Q725508","display_name":"Somatic cell","level":3,"score":0.7465089559555054},{"id":"https://openalex.org/C2992936677","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Plant biology","level":2,"score":0.7301175594329834},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5249821543693542},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4975126087665558},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.47241225838661194},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.4467834532260895},{"id":"https://openalex.org/C42407357","wikidata":"https://www.wikidata.org/wiki/Q521","display_name":"Physiology","level":1,"score":0.38667571544647217},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2722397446632385},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13096925616264343},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.09631305932998657}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","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":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.12688/f1000research.74395.1","doi":"https://doi.org/10.12688/f1000research.74395.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.74395.1","pdf_url":"https://f1000research.com/articles/10-1111/v1/pdf","source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-70","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357","https://openalex.org/P4310320547"],"host_organization_lineage_names":["Faculty of 1000","Taylor & Francis"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"F1000Research","raw_type":"journal-article"},{"id":"doi:10.12688/f1000research.74395.2","doi":"https://doi.org/10.12688/f1000research.74395.2","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.74395.2","pdf_url":null,"source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-70","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357","https://openalex.org/P4310320547"],"host_organization_lineage_names":["Faculty of 1000","Taylor & Francis"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"F1000Research","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9755755","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9755755","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"F1000Res","raw_type":"Text"},{"id":"pmid:36569594","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36569594","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,"listed_in":[],"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":"F1000Research","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.12688/f1000research.74395.1","doi":"https://doi.org/10.12688/f1000research.74395.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.74395.1","pdf_url":"https://f1000research.com/articles/10-1111/v1/pdf","source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-70","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357","https://openalex.org/P4310320547"],"host_organization_lineage_names":["Faculty of 1000","Taylor & Francis"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"F1000Research","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.6240000128746033,"id":"https://metadata.un.org/sdg/3"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G1826421787","display_name":null,"funder_award_id":"AwardNumberU41HG003751(GW)","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G2815737439","display_name":"Reactome: An Open Knowledgebase of Human Pathways","funder_award_id":"U41HG003751","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G3219587245","display_name":null,"funder_award_id":"24317","funder_id":"https://openalex.org/F4320323054","funder_display_name":"Associazione Italiana per la Ricerca sul Cancro"},{"id":"https://openalex.org/G5623175075","display_name":"Reactome IDG portal: Pathway-based analysis and visualization of understudied human proteins","funder_award_id":"U01CA239069","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G7580648242","display_name":null,"funder_award_id":"(MFAG2020-ID.24317)","funder_id":"https://openalex.org/F4320323054","funder_display_name":"Associazione Italiana per la Ricerca sul Cancro"},{"id":"https://openalex.org/G868862665","display_name":null,"funder_award_id":"MFAG 2020","funder_id":"https://openalex.org/F4320323054","funder_display_name":"Associazione Italiana per la Ricerca sul Cancro"},{"id":"https://openalex.org/G9000862757","display_name":"Research Training in Biomedical Informatics and Data Science at Oregon Health & Science University","funder_award_id":"T15LM007088","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"}],"funders":[{"id":"https://openalex.org/F4320308269","display_name":"Alexander von Humboldt-Stiftung","ror":"https://ror.org/012kf4317"},{"id":"https://openalex.org/F4320311012","display_name":"Scuola Normale Superiore","ror":"https://ror.org/03aydme10"},{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321873","display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca","ror":"https://ror.org/0166hxq48"},{"id":"https://openalex.org/F4320323054","display_name":"Associazione Italiana per la Ricerca sul Cancro","ror":"https://ror.org/02g2x7380"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3208551392.pdf","grobid_xml":"https://content.openalex.org/works/W3208551392.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1876009826","https://openalex.org/W1935434993","https://openalex.org/W1940319397","https://openalex.org/W1956577542","https://openalex.org/W1965379872","https://openalex.org/W2008472008","https://openalex.org/W2039473152","https://openalex.org/W2058539819","https://openalex.org/W2062533676","https://openalex.org/W2065121554","https://openalex.org/W2097508475","https://openalex.org/W2104300069","https://openalex.org/W2108377388","https://openalex.org/W2110065044","https://openalex.org/W2121906867","https://openalex.org/W2139994096","https://openalex.org/W2144954642","https://openalex.org/W2158714788","https://openalex.org/W2168303063","https://openalex.org/W2230320310","https://openalex.org/W2529097733","https://openalex.org/W2593881435","https://openalex.org/W2782153240","https://openalex.org/W2789454947","https://openalex.org/W2796408191","https://openalex.org/W2894573839","https://openalex.org/W2898210859","https://openalex.org/W2948545594","https://openalex.org/W2950796639","https://openalex.org/W2950945059","https://openalex.org/W2962854624","https://openalex.org/W3002310680","https://openalex.org/W3004883393","https://openalex.org/W3008303614","https://openalex.org/W3138855639","https://openalex.org/W3199799076","https://openalex.org/W4231254854","https://openalex.org/W4288076435","https://openalex.org/W6912844257","https://openalex.org/W6948928281","https://openalex.org/W6950643201","https://openalex.org/W6968774469"],"related_works":["https://openalex.org/W6920652380","https://openalex.org/W4323349878","https://openalex.org/W7149704258","https://openalex.org/W4306914612","https://openalex.org/W2331480251","https://openalex.org/W2133730856","https://openalex.org/W7169776434","https://openalex.org/W2186667705","https://openalex.org/W4285214844","https://openalex.org/W2529097733"],"abstract_inverted_index":{"Background:":[0],"Considering":[1],"protein":[2,77],"mutations":[3,84,110,142],"in":[4,25,64,94,155,163,227],"their":[5,12],"biological":[6],"context":[7],"is":[8,221],"essential":[9],"for":[10,55,176,195,245],"understanding":[11],"functional":[13],"impact,":[14],"interpretation":[15],"of":[16,21,34,42,101,173,248],"high-dimensional":[17],"datasets":[18],"and":[19,59,71,76,92,165,233],"development":[20],"effective":[22],"targeted":[23],"therapies":[24],"personalized":[26],"medicine.":[27],"Methods:":[28],"We":[29,81,98],"combined":[30],"the":[31,40,61,170],"curated":[32],"knowledge":[33],"biochemical":[35,231],"reactions":[36,72,91,232],"from":[37,46,69,85,223],"Reactome":[38],"with":[39,149],"analysis":[41,62,180],"interaction-mediating":[43],"3D":[44,78,217],"interfaces":[45],"Mechismo.":[47],"In":[48,201],"addition,":[49],"we":[50,139,203],"provided":[51],"a":[52,65,206],"software":[53],"tool":[54],"users":[56],"to":[57,73,113,118,209,237],"explore":[58],"browse":[60],"results":[63],"multi-scale":[66,207],"perspective":[67],"starting":[68],"pathways":[70,93,162],"protein-protein":[74,215],"interactions":[75],"structures.":[79,218],"Results:":[80],"analyzed":[82],"somatic":[83],"TCGA,":[86],"revealing":[87],"several":[88,183],"significantly":[89,147],"impacted":[90],"specific":[95,156],"cancer":[96,115,157,167],"types.":[97],"found":[99,140],"examples":[100],"genes":[102],"not":[103],"yet":[104],"listed":[105],"as":[106],"oncodrivers,":[107,127],"whose":[108],"rare":[109],"were":[111],"predicted":[112],"affect":[114],"processes":[116,123,133,145,185],"similarly":[117],"known":[119,126],"oncodrivers.":[120],"Some":[121],"identified":[122],"lack":[124],"any":[125],"which":[128],"suggests":[129],"potentially":[130],"new":[131,196],"cancer-related":[132],"(e.g.":[134,159,186,241],"complement":[135],"cascade":[136],"reactions).":[137],"Furthermore,":[138],"that":[141],"perturbing":[143],"certain":[144],"are":[146],"associated":[148],"distinct":[150],"phenotypes":[151],"(i.e.":[152],"survival":[153],"time)":[154],"types":[158,240,247],"PIK3CA":[160],"centered":[161],"LGG":[164],"UCEC":[166],"types),":[168],"suggesting":[169],"translational":[171],"potential":[172],"our":[174],"approach":[175,208,220],"patient":[177],"stratification.":[178],"Our":[179,219],"also":[181],"uncovered":[182],"druggable":[184],"GPCR":[187],"signalling":[188],"pathways)":[189],"containing":[190],"enriched":[191],"reactions,":[192],"providing":[193],"support":[194],"off-label":[197],"therapeutic":[198],"options.":[199],"Conclusions:":[200],"summary,":[202],"have":[204],"established":[205],"study":[210],"genetic":[211],"variants":[212],"based":[213],"on":[214,230],"interaction":[216],"different":[222],"previously":[224],"published":[225],"studies":[226],"its":[228],"focus":[229],"can":[234],"be":[235],"applied":[236],"other":[238],"data":[239],"post-translational":[242],"modifications)":[243],"collected":[244],"many":[246],"disease.":[249]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2021-11-08T00:00:00"}