{"id":"https://openalex.org/W4387141138","doi":"https://doi.org/10.1186/s40537-023-00826-0","title":"Dissecting tumor antigens and immune subtypes for mRNA vaccine development in breast cancer","display_name":"Dissecting tumor antigens and immune subtypes for mRNA vaccine development in breast cancer","publication_year":2023,"publication_date":"2023-09-28","ids":{"openalex":"https://openalex.org/W4387141138","doi":"https://doi.org/10.1186/s40537-023-00826-0"},"language":"en","primary_location":{"id":"doi:10.1186/s40537-023-00826-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s40537-023-00826-0","pdf_url":"https://journalofbigdata.springeropen.com/counter/pdf/10.1186/s40537-023-00826-0","source":{"id":"https://openalex.org/S2737955091","display_name":"Journal Of Big Data","issn_l":"2196-1115","issn":["2196-1115"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Big Data","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journalofbigdata.springeropen.com/counter/pdf/10.1186/s40537-023-00826-0","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100383613","display_name":"Lang Li","orcid":"https://orcid.org/0000-0002-2946-7021"},"institutions":[{"id":"https://openalex.org/I4210110379","display_name":"Jining Traditional Chinese Medicine Hospital","ror":"https://ror.org/027f56t09","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210110379"]},{"id":"https://openalex.org/I114539943","display_name":"Zhejiang Chinese Medical University","ror":"https://ror.org/04epb4p87","country_code":"CN","type":"education","lineage":["https://openalex.org/I114539943"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Lang Li","raw_affiliation_strings":["Department of Hematology, Jinhua Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, 438 West Shuangxi Road, Jinhua, 321017, China","Department of Hematology, Jinhua Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Jinhua, China"],"affiliations":[{"raw_affiliation_string":"Department of Hematology, Jinhua Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, 438 West Shuangxi Road, Jinhua, 321017, China","institution_ids":["https://openalex.org/I4210110379"]},{"raw_affiliation_string":"Department of Hematology, Jinhua Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Jinhua, China","institution_ids":["https://openalex.org/I114539943"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101249862","display_name":"Lvyuan He","orcid":"https://orcid.org/0009-0004-0514-1686"},"institutions":[{"id":"https://openalex.org/I4210110379","display_name":"Jining Traditional Chinese Medicine Hospital","ror":"https://ror.org/027f56t09","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210110379"]},{"id":"https://openalex.org/I114539943","display_name":"Zhejiang Chinese Medical University","ror":"https://ror.org/04epb4p87","country_code":"CN","type":"education","lineage":["https://openalex.org/I114539943"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lvyuan He","raw_affiliation_strings":["Department of Hematology, Jinhua Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, 438 West Shuangxi Road, Jinhua, 321017, China","Department of Hematology, Jinhua Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Jinhua, China"],"affiliations":[{"raw_affiliation_string":"Department of Hematology, Jinhua Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, 438 West Shuangxi Road, Jinhua, 321017, China","institution_ids":["https://openalex.org/I4210110379"]},{"raw_affiliation_string":"Department of Hematology, Jinhua Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Jinhua, China","institution_ids":["https://openalex.org/I114539943"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061191217","display_name":"Ying Zhu","orcid":"https://orcid.org/0000-0002-5502-3571"},"institutions":[{"id":"https://openalex.org/I4210110379","display_name":"Jining Traditional Chinese Medicine Hospital","ror":"https://ror.org/027f56t09","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210110379"]},{"id":"https://openalex.org/I114539943","display_name":"Zhejiang Chinese Medical University","ror":"https://ror.org/04epb4p87","country_code":"CN","type":"education","lineage":["https://openalex.org/I114539943"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ying Zhu","raw_affiliation_strings":["Department of Hematology, Jinhua Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, 438 West Shuangxi Road, Jinhua, 321017, China","Department of Hematology, Jinhua Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Jinhua, China"],"affiliations":[{"raw_affiliation_string":"Department of Hematology, Jinhua Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, 438 West Shuangxi Road, Jinhua, 321017, China","institution_ids":["https://openalex.org/I4210110379"]},{"raw_affiliation_string":"Department of Hematology, Jinhua Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Jinhua, China","institution_ids":["https://openalex.org/I114539943"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100383613"],"corresponding_institution_ids":["https://openalex.org/I114539943","https://openalex.org/I4210110379"],"apc_list":{"value":1060,"currency":"GBP","value_usd":1300},"apc_paid":{"value":1060,"currency":"GBP","value_usd":1300},"fwci":0.4665,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.74078928,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":"10","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10158","display_name":"Cancer Immunotherapy and Biomarkers","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10158","display_name":"Cancer Immunotherapy and Biomarkers","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9986000061035156,"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/T11297","display_name":"Ferroptosis and cancer prognosis","score":0.9976999759674072,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.7220233082771301},{"id":"https://openalex.org/keywords/breast-cancer","display_name":"Breast cancer","score":0.6927903890609741},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.4946384131908417},{"id":"https://openalex.org/keywords/immunotherapy","display_name":"Immunotherapy","score":0.48394206166267395},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4272944927215576},{"id":"https://openalex.org/keywords/cancer-vaccine","display_name":"Cancer vaccine","score":0.4197573661804199},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.4196944236755371},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4103090167045593},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.4046788215637207},{"id":"https://openalex.org/keywords/cancer-research","display_name":"Cancer research","score":0.36144158244132996},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.3523843586444855},{"id":"https://openalex.org/keywords/oncology","display_name":"Oncology","score":0.3342217803001404},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3205946385860443},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16435253620147705}],"concepts":[{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.7220233082771301},{"id":"https://openalex.org/C530470458","wikidata":"https://www.wikidata.org/wiki/Q128581","display_name":"Breast cancer","level":3,"score":0.6927903890609741},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.4946384131908417},{"id":"https://openalex.org/C2777701055","wikidata":"https://www.wikidata.org/wiki/Q1427096","display_name":"Immunotherapy","level":3,"score":0.48394206166267395},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4272944927215576},{"id":"https://openalex.org/C2778378633","wikidata":"https://www.wikidata.org/wiki/Q2378309","display_name":"Cancer vaccine","level":4,"score":0.4197573661804199},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.4196944236755371},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4103090167045593},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.4046788215637207},{"id":"https://openalex.org/C502942594","wikidata":"https://www.wikidata.org/wiki/Q3421914","display_name":"Cancer research","level":1,"score":0.36144158244132996},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.3523843586444855},{"id":"https://openalex.org/C143998085","wikidata":"https://www.wikidata.org/wiki/Q162555","display_name":"Oncology","level":1,"score":0.3342217803001404},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3205946385860443},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16435253620147705}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1186/s40537-023-00826-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s40537-023-00826-0","pdf_url":"https://journalofbigdata.springeropen.com/counter/pdf/10.1186/s40537-023-00826-0","source":{"id":"https://openalex.org/S2737955091","display_name":"Journal Of Big Data","issn_l":"2196-1115","issn":["2196-1115"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Big Data","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:4dfc02ac90af4a2da97d7cbf8de520f5","is_oa":true,"landing_page_url":"https://doaj.org/article/4dfc02ac90af4a2da97d7cbf8de520f5","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":"Journal of Big Data, Vol 10, Iss 1, Pp 1-21 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s40537-023-00826-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s40537-023-00826-0","pdf_url":"https://journalofbigdata.springeropen.com/counter/pdf/10.1186/s40537-023-00826-0","source":{"id":"https://openalex.org/S2737955091","display_name":"Journal Of Big Data","issn_l":"2196-1115","issn":["2196-1115"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Big Data","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.47999998927116394,"display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4387141138.pdf"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1966327575","https://openalex.org/W1966975305","https://openalex.org/W2004979714","https://openalex.org/W2028433016","https://openalex.org/W2034639401","https://openalex.org/W2035618305","https://openalex.org/W2052193554","https://openalex.org/W2062398277","https://openalex.org/W2084370215","https://openalex.org/W2115462905","https://openalex.org/W2120426523","https://openalex.org/W2123879591","https://openalex.org/W2149441684","https://openalex.org/W2159707944","https://openalex.org/W2169353806","https://openalex.org/W2375577403","https://openalex.org/W2533508881","https://openalex.org/W2582033455","https://openalex.org/W2782708334","https://openalex.org/W2796207838","https://openalex.org/W2799465346","https://openalex.org/W2896872272","https://openalex.org/W2917464640","https://openalex.org/W2937441321","https://openalex.org/W2946657092","https://openalex.org/W3002154893","https://openalex.org/W3011781411","https://openalex.org/W3052573234","https://openalex.org/W3080277530","https://openalex.org/W3105159289","https://openalex.org/W3107457426","https://openalex.org/W3128646645","https://openalex.org/W3134481517","https://openalex.org/W3134487827","https://openalex.org/W3147728334","https://openalex.org/W3156394540","https://openalex.org/W3203575974","https://openalex.org/W3209991562","https://openalex.org/W4200578065","https://openalex.org/W4210816705","https://openalex.org/W4283080644","https://openalex.org/W4285507696","https://openalex.org/W4293579374","https://openalex.org/W4297154080","https://openalex.org/W4311662686"],"related_works":["https://openalex.org/W2220102944","https://openalex.org/W4360983034","https://openalex.org/W2409441623","https://openalex.org/W1996150995","https://openalex.org/W2224319365","https://openalex.org/W4210976760","https://openalex.org/W1974496092","https://openalex.org/W2275222446","https://openalex.org/W2071315909","https://openalex.org/W4230843304"],"abstract_inverted_index":{"Abstract":[0],"Purposes":[1],"Cancer":[2,57,68],"mRNA":[3,17,34,294,308,317],"vaccines":[4,18],"are":[5,288,303],"a":[6,10,38,304,313],"promising":[7],"strategy":[8],"and":[9,37,49,62,77,93,170,177,183,200,209,253,286,324],"hot":[11],"topic":[12],"in":[13,188,205,246,266],"cancer":[14,21],"immunotherapy.":[15],"However,":[16],"for":[19,33,43,117,293,307,322],"breast":[20],"(BRCA)":[22],"remain":[23],"undeveloped.":[24],"This":[25,310],"study":[26,311],"aimed":[27],"to":[28,84,110,127,141,153,218,233],"identify":[29,85,128,154],"potential":[30,160,290],"tumor":[31,161,291],"antigens":[32,292],"vaccine":[35,295,318],"development":[36,296],"population":[39,306,320],"with":[40,98,174,214,229,276,297,300],"BRCA":[41,212,267],"suitable":[42,305],"vaccination.":[44,309],"Methods":[45],"Gene":[46],"expression":[47,257],"profiles":[48],"the":[50,54,75,99,207,289],"clinical":[51],"information":[52],"of":[53,66,113],"TCGA-BRCA":[55,208],"(the":[56],"Genome":[58],"Atlas":[59],"Breast":[60,67],"Cancer)":[61],"METABRIC":[63,210],"(Molecular":[64],"Taxonomy":[65],"International":[69],"Consortium)":[70],"cohorts":[71],"were":[72,96,186,203,244],"downloaded":[73],"from":[74],"TCGA":[76],"cBioPortal":[78,81],"databases,":[79],"respectively.":[80],"was":[82,108,125,139,151],"used":[83,126],"mutant":[86],"genes.":[87],"DEG":[88],"(differentially":[89],"expressed":[90],"gene)":[91],"identification":[92],"survival":[94],"analysis":[95,137],"performed":[97,152],"GEPIA2":[100],"tool.":[101],"ssGSEA":[102],"(single-sample":[103],"gene":[104,156,274],"set":[105],"enrichment":[106],"analysis)":[107,150],"applied":[109],"estimate":[111],"abundances":[112],"28":[114],"immune":[115,144,155,197,223,238,260,264,273],"cells":[116],"each":[118],"sample.":[119],"An":[120],"unsupervised":[121],"consensus":[122],"clustering":[123],"algorithm":[124,138],"ISs":[129,191],"(immune":[130,255],"subtypes).":[131],"A":[132],"graph":[133],"learning-based":[134],"dimensionality":[135],"reduction":[136],"utilized":[140],"construct":[142],"an":[143,222,237,263],"landscape.":[145],"WGCNA":[146],"(weighted":[147],"correlation":[148],"network":[149],"modules.":[157],"Results":[158],"Four":[159],"antigens,":[162],"i.e.,":[163],"SLC7A5":[164,281],",":[165,167,169,172,282,285],"CHPF":[166],"CCNE1":[168,284],"CENPW":[171,287],"associated":[173],"poor":[175,219],"prognosis":[176,220,235,325],"APCs":[178],"(antigen-presenting":[179],"cells)":[180],"among":[181],"overexpressed":[182],"mutated":[184],"genes":[185],"identified":[187,271],"BRCA.":[189,298],"Two":[190],"(IS1-2)":[192],"characterized":[193],"by":[194],"distinct":[195],"clinical,":[196],"cell":[198,250],"infiltration,":[199],"molecular":[201],"features":[202],"observed":[204,245],"both":[206],"cohorts.":[211],"patients":[213,228],"IS2":[215,301],"tumors":[216,231,243,302],"related":[217,232],"had":[221,236],"\"hot\"":[224],"phenotype,":[225],"while":[226],"those":[227],"IS1":[230],"superior":[234],"\"cold\"":[239],"phenotype.":[240],"Distinct":[241],"IS":[242],"different":[247,277],"ICD":[248],"(immunogenic":[249],"death":[251],"modulator)":[252],"ICP":[254],"checkpoint)":[256],"profiles.":[258],"The":[259],"landscape":[261],"showed":[262],"distribution":[265],"patients.":[268],"Additionally,":[269],"we":[270],"2":[272],"modules":[275],"biological":[278],"functions.":[279],"Conclusions":[280],"CHPF,":[283],"Patients":[299],"provides":[312],"new":[314],"insight":[315],"into":[316],"development,":[319],"selection":[321],"vaccination,":[323],"prediction.":[326]},"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2026-03-18T14:38:29.013473","created_date":"2025-10-10T00:00:00"}
