{"id":"https://openalex.org/W2905130244","doi":"https://doi.org/10.1093/bib/bby105","title":"dbCPM: a manually curated database for exploring the cancer passenger mutations","display_name":"dbCPM: a manually curated database for exploring the cancer passenger mutations","publication_year":2018,"publication_date":"2018-10-05","ids":{"openalex":"https://openalex.org/W2905130244","doi":"https://doi.org/10.1093/bib/bby105","mag":"2905130244","pmid":"https://pubmed.ncbi.nlm.nih.gov/30379998"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bby105","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bby105","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044447237","display_name":"Zhenyu Yue","orcid":"https://orcid.org/0000-0002-9370-2540"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhenyu Yue","raw_affiliation_strings":["Institute of Physical Science and Information Technology, School of Computer Science and Technology, Anhui University, Hefei, Anhui, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Physical Science and Information Technology, School of Computer Science and Technology, Anhui University, Hefei, Anhui, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102013843","display_name":"Le Zhao","orcid":"https://orcid.org/0000-0003-3480-2493"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Le Zhao","raw_affiliation_strings":["Institute of Physical Science and Information Technology, School of Computer Science and Technology, Anhui University, Hefei, Anhui, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Physical Science and Information Technology, School of Computer Science and Technology, Anhui University, Hefei, Anhui, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065943710","display_name":"Junfeng Xia","orcid":"https://orcid.org/0000-0003-3024-1705"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Junfeng Xia","raw_affiliation_strings":["Institute of Physical Science and Information Technology, School of Computer Science and Technology, Anhui University, Hefei, Anhui, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Physical Science and Information Technology, School of Computer Science and Technology, Anhui University, Hefei, Anhui, China","institution_ids":["https://openalex.org/I143868143"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5065943710"],"corresponding_institution_ids":["https://openalex.org/I143868143"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.7897,"has_fulltext":false,"cited_by_count":21,"citation_normalized_percentile":{"value":0.67528551,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"21","issue":"1","first_page":"309","last_page":"317"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9998000264167786,"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"}},"topics":[{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9998000264167786,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9983000159263611,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.9972000122070312,"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/missense-mutation","display_name":"Missense mutation","score":0.9085434675216675},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6160991191864014},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.6117681860923767},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5750592947006226},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.522692084312439},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49961209297180176},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4557984471321106},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4543920159339905},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.4479861557483673},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.43158653378486633},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4257831275463104},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4078139662742615},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.24256378412246704},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.06152591109275818},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.05969777703285217}],"concepts":[{"id":"https://openalex.org/C75563809","wikidata":"https://www.wikidata.org/wiki/Q2656896","display_name":"Missense mutation","level":4,"score":0.9085434675216675},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6160991191864014},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.6117681860923767},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5750592947006226},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.522692084312439},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49961209297180176},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4557984471321106},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4543920159339905},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.4479861557483673},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.43158653378486633},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4257831275463104},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4078139662742615},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.24256378412246704},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.06152591109275818},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.05969777703285217},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bby105","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bby105","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30379998","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30379998","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2483327137","display_name":"\u8f7d\u80fd\u7c92\u5b50\u5bf9\u5173\u952e\u751f\u7269\u9776\u7684\u5206\u5b50\u8c03\u63a7\u673a\u5236\u4e0e\u5e94\u7528\u57fa\u7840\u7814\u7a76","funder_award_id":"11835014","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5573161910","display_name":null,"funder_award_id":"61672037","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"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":89,"referenced_works":["https://openalex.org/W1128147987","https://openalex.org/W1575166469","https://openalex.org/W1596947964","https://openalex.org/W1971435235","https://openalex.org/W1976815080","https://openalex.org/W1980740976","https://openalex.org/W1982993862","https://openalex.org/W1997338248","https://openalex.org/W2002052142","https://openalex.org/W2009634860","https://openalex.org/W2016193168","https://openalex.org/W2018130645","https://openalex.org/W2022306674","https://openalex.org/W2031975549","https://openalex.org/W2059145105","https://openalex.org/W2059300459","https://openalex.org/W2063632443","https://openalex.org/W2072572998","https://openalex.org/W2087025655","https://openalex.org/W2095659509","https://openalex.org/W2098650870","https://openalex.org/W2102140136","https://openalex.org/W2111326065","https://openalex.org/W2112604819","https://openalex.org/W2114029728","https://openalex.org/W2118621341","https://openalex.org/W2122732537","https://openalex.org/W2129016996","https://openalex.org/W2132312350","https://openalex.org/W2145191876","https://openalex.org/W2146841526","https://openalex.org/W2154139219","https://openalex.org/W2159092541","https://openalex.org/W2171777347","https://openalex.org/W2174602966","https://openalex.org/W2224056471","https://openalex.org/W2259938310","https://openalex.org/W2261193987","https://openalex.org/W2308989383","https://openalex.org/W2309021002","https://openalex.org/W2526413677","https://openalex.org/W2614443510","https://openalex.org/W2754300472","https://openalex.org/W2781525129","https://openalex.org/W2790516087","https://openalex.org/W2796408191","https://openalex.org/W4233120011","https://openalex.org/W4236214948","https://openalex.org/W4299944458","https://openalex.org/W4300886089","https://openalex.org/W6633658626","https://openalex.org/W6635826468","https://openalex.org/W6642961773","https://openalex.org/W6644601165","https://openalex.org/W6645418422","https://openalex.org/W6646374428","https://openalex.org/W6649389396","https://openalex.org/W6650582943","https://openalex.org/W6652683183","https://openalex.org/W6654550239","https://openalex.org/W6654866624","https://openalex.org/W6658220875","https://openalex.org/W6665135625","https://openalex.org/W6665783544","https://openalex.org/W6666526701","https://openalex.org/W6668385591","https://openalex.org/W6674236492","https://openalex.org/W6674660197","https://openalex.org/W6675104955","https://openalex.org/W6676588614","https://openalex.org/W6676818494","https://openalex.org/W6677089086","https://openalex.org/W6677706050","https://openalex.org/W6678235093","https://openalex.org/W6679948235","https://openalex.org/W6681744673","https://openalex.org/W6681872996","https://openalex.org/W6683552020","https://openalex.org/W6685387098","https://openalex.org/W6689099039","https://openalex.org/W6692805499","https://openalex.org/W6698177866","https://openalex.org/W6698247574","https://openalex.org/W6727846345","https://openalex.org/W6738337739","https://openalex.org/W6744655623","https://openalex.org/W6748676849","https://openalex.org/W6749511434","https://openalex.org/W6832027530"],"related_works":["https://openalex.org/W3004443428","https://openalex.org/W2361861616","https://openalex.org/W4361004911","https://openalex.org/W2625862723","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W1971719088","https://openalex.org/W2612068534","https://openalex.org/W2069150591","https://openalex.org/W4232163425"],"abstract_inverted_index":{"While":[0],"recently":[1],"emergent":[2],"driver":[3,81,116],"mutation":[4,16,60,90],"data":[5,159,178],"sets":[6,19],"are":[7,24],"available":[8,200],"for":[9,161,180,192],"developing":[10,162],"computational":[11],"methods":[12],"to":[13,143],"predict":[14],"cancer":[15,194],"effects,":[17],"benchmark":[18,177],"focusing":[20],"on":[21,122],"passenger":[22,47,73,98,114],"mutations":[23,48,74,82,99],"largely":[25],"missing.":[26],"Here,":[27],"we":[28,68],"developed":[29],"a":[30,51,156,163,176,189],"comprehensive":[31],"literature-based":[32],"database":[33],"of":[34,54,71,87,146],"Cancer":[35],"Passenger":[36],"Mutations":[37],"(dbCPM),":[38],"which":[39,153],"contains":[40],"941":[41],"experimentally":[42],"supported":[43],"and":[44,83,108,115,182,186],"978":[45],"putative":[46],"derived":[49],"from":[50],"manual":[52],"curation":[53],"the":[55,58,62,66,79,85,96,113,123,128,144,172,193],"literature.":[56],"Using":[57],"missense":[59,72,80,97],"data,":[61],"largest":[63],"group":[64],"in":[65,111],"dbCPM,":[67],"explored":[69],"patterns":[70],"by":[75],"comparing":[76],"them":[77],"with":[78,103,150],"assessed":[84],"performance":[86],"four":[88],"cancer-focused":[89],"effect":[91],"predictors.":[92],"We":[93,169],"found":[94],"that":[95,155,171],"showed":[100],"significant":[101],"differences":[102],"drivers":[104],"at":[105,202],"multiple":[106],"levels,":[107],"several":[109],"appeared":[110],"both":[112],"categories,":[117],"showing":[118],"pleiotropic":[119],"functions":[120],"depending":[121],"tumor":[124],"context.":[125],"Although":[126],"all":[127],"predictors":[129],"displayed":[130],"good":[131],"true":[132,136],"positive":[133],"rates,":[134],"their":[135],"negative":[137,147,158],"rates":[138],"were":[139],"relatively":[140],"low":[141],"due":[142],"lack":[145],"training":[148],"samples":[149],"experimental":[151],"evidence,":[152],"suggests":[154],"suitable":[157],"set":[160,179],"more":[164],"robust":[165],"methodology":[166],"is":[167,198],"needed.":[168],"hope":[170],"dbCPM":[173,197],"will":[174],"be":[175],"improving":[181],"evaluating":[183],"prediction":[184],"algorithms":[185],"serve":[187],"as":[188],"valuable":[190],"resource":[191],"research":[195],"community.":[196],"freely":[199],"online":[201],"http://bioinfo.ahu.edu.cn:8080/dbCPM.":[203]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":4}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
