{"doi":"10.1093/nar/gkae1098","title":"OncoSplicing 3.0: an updated database for identifying RBPs regulating alternative splicing events in cancers","abstract":"<jats:title>Abstract</jats:title>\n               <jats:p>Alternative splicing (AS) is a crucial mechanism to regulate gene expression and protein complexity. RNA-binding proteins (RBPs) play an important role in regulating abnormal alternative splicing in cancers. However, few resources are available to identify specific RBPs responsible for regulating individual AS event. We have developed the OncoSplicing database for integrative analysis of clinically relevant alternative splicing events in TCGA cancers. Here, we further updated the OncoSplicing database by performing correlation analysis between the splicing and mRNA expression data from the TCGA cancers or GTEx tissues, mapping known RNA-binding motifs and eCLIP-seq peaks to all AS events, conducting splicing analysis for RNA-seq data from RBP perturbation experiments in the ENCODE project, and integrating exon and intron sequences for each AS event. With this updated database, users can easily identify potential RBPs responsible for the queried AS event and obtain sequences to design AS-specific primers and minigene constructs for experiment validation. Overall, compared to the previous version, the substantially updated OncoSplicing database (www.oncosplicing.com) offers a more valuable resource for users to identify RBPs responsible for regulating alternative splicing events in cancers.</jats:p>","journal":"Nucleic Acids Research","year":2025,"id":637604,"datarank":0.3958585994422889,"base_score":2.639057329615259,"endowment":2.639057329615259,"self_citation_contribution":0.3958585994422889,"citation_network_contribution":0.0,"self_endowment_contribution":0.3958585994422889,"citer_contribution":0.0,"corpus_percentile":53.9,"corpus_rank":6218,"citation_count":13,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":854265,"name":"Kai Liu","orcid":"0000-0001-9351-1640","position":1,"is_corresponding":false},{"id":419630,"name":"Zhenzhen Xu","orcid":"0000-0002-8755-8597","position":2,"is_corresponding":false},{"id":582684,"name":"Bo Li","orcid":"0000-0001-8782-2485","position":3,"is_corresponding":false},{"id":1307375,"name":"Xiaoliang Wu","orcid":"0009-0003-9643-5518","position":4,"is_corresponding":false},{"id":1655685,"name":"Ruixin Fan","orcid":null,"position":5,"is_corresponding":false},{"id":1655689,"name":"Xiangyang Yao","orcid":null,"position":6,"is_corresponding":false},{"id":491520,"name":"Huahui Wu","orcid":null,"position":7,"is_corresponding":false},{"id":926982,"name":"Chen Duan","orcid":"0009-0005-6337-8064","position":8,"is_corresponding":false},{"id":942283,"name":"Yan Gong","orcid":"0000-0002-4805-0459","position":9,"is_corresponding":false},{"id":723238,"name":"Ke Chen","orcid":"0000-0003-2089-1288","position":10,"is_corresponding":false},{"id":828306,"name":"Jin Zeng","orcid":null,"position":11,"is_corresponding":false},{"id":522343,"name":"Lu Li","orcid":"0009-0000-3747-6203","position":12,"is_corresponding":false},{"id":1327847,"name":"Hua Xu","orcid":"0000-0002-7401-307X","position":13,"is_corresponding":false},{"id":1023160,"name":"Yangjun Zhang","orcid":"0000-0003-1070-6210","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"OncoSplicing 3.0: an updated database for identifying RBPs regulating alternative splicing events in cancers","abstract":"<jats:title>Abstract</jats:title>\n               <jats:p>Alternative splicing (AS) is a crucial mechanism to regulate gene expression and protein complexity. RNA-binding proteins (RBPs) play an important role in regulating abnormal alternative splicing in cancers. However, few resources are available to identify specific RBPs responsible for regulating individual AS event. We have developed the OncoSplicing database for integrative analysis of clinically relevant alternative splicing events in TCGA cancers. Here, we further updated the OncoSplicing database by performing correlation analysis between the splicing and mRNA expression data from the TCGA cancers or GTEx tissues, mapping known RNA-binding motifs and eCLIP-seq peaks to all AS events, conducting splicing analysis for RNA-seq data from RBP perturbation experiments in the ENCODE project, and integrating exon and intron sequences for each AS event. With this updated database, users can easily identify potential RBPs responsible for the queried AS event and obtain sequences to design AS-specific primers and minigene constructs for experiment validation. Overall, compared to the previous version, the substantially updated OncoSplicing database (www.oncosplicing.com) offers a more valuable resource for users to identify RBPs responsible for regulating alternative splicing events in cancers.</jats:p>","is_dataset_classified":null,"base_score":2.639057329615259,"endowment":2.639057329615259,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"39558172","pmcid":"PMC11701682","openalex_id":"https://openalex.org/W4404511370","authors":[],"funders":[{"funder_name":"National Natural Science Foundation of China","grant_id":"82070726","title":null},{"funder_name":"National Natural Science Foundation of China","grant_id":"82270803","title":null},{"funder_name":"National Natural Science Foundation of China","grant_id":"82203365","title":null},{"funder_name":"China Postdoctoral Science Foundation","grant_id":"2022M722464","title":null},{"funder_name":"Jiangxi Provincial Natural Science Foundation","grant_id":"20232BAB206090","title":null}],"total_grants":5,"fwci":2.1029,"citation_percentile":0.87948203,"influential_citations":0,"citation_trend":[{"year":2025,"count":6},{"year":2026,"count":7}],"oa_status":"gold","license":"cc-by-nc","oa_locations":[{"url":"https://doi.org/10.1093/nar/gkae1098","host_type":"journal"},{"url":"https://doi.org/10.1093/nar/gkae1098","host_type":"publisher"},{"url":"https://academic.oup.com/nar/article-pdf/53/D1/D1460/60743848/gkae1098.pdf","host_type":"publisher"},{"url":"https://pubmed.ncbi.nlm.nih.gov/39558172","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11701682","host_type":"repository"},{"url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11701682/pdf/gkae1098.pdf","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC11701682","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC11701682?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["RNA Research and Splicing","RNA modifications and cancer","RNA and protein synthesis mechanisms","Alternative Splicing","Humans","Neoplasms","RNA-Binding Proteins","Databases, Genetic","Exons","RNA, Messenger","Gene Expression Regulation, Neoplastic","Introns"],"mesh_terms":["Exons","Humans","Introns","Neoplasms","RNA, Messenger","Gene Expression Regulation, Neoplastic","RNA-Binding Proteins","Alternative Splicing","Databases, Genetic"],"keywords":["Minigene","RNA splicing","Biology","Alternative splicing","RNA-binding protein","Computational biology","Intron","Exon","RNA-Seq","Genetics","Gene expression profiling","Gene","Transcriptome","Database","Gene expression","RNA","Computer science"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Partnerships for the goals"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-06T19:13:28.701788Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}