{"doi":"10.1016/j.xpro.2022.101651","title":"An expression-based variant impact phenotyping protocol to predict the impact of gene variants in cell lines","abstract":"We describe a bioinformatics protocol for eVIP2 (expression-based variant impact phenotyping). eVIP2 can predict a gene variant's functional impact by comparing gene expression signatures induced by introduction of wild-type versus mutant cDNAs in cell lines. The predicted functional outcomes of the variants include gain-of-function, loss-of-function, change-of-function, or neutral. eVIP2 improves upon eVIP by being applicable to RNA-seq data and providing pathway-level functional predictions for each mutation. Here, we detail how to run eVIP2 on RNA-seq data from two RNF43 variants. For complete details on the use and execution of this protocol, please refer to Thornton et al. (2021).","journal":"Cáritas","year":2022,"id":310963,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9582,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1007273,"name":"Manoj Tumu","orcid":null,"position":1,"is_corresponding":false},{"id":13299,"name":"Angela N. Brooks","orcid":"0000-0002-7898-3073","position":2,"is_corresponding":false},{"id":356523,"name":"Alexis M. Thornton","orcid":"0000-0002-7987-2543","position":0,"is_corresponding":true}],"reference_count":15,"raw_metadata":null,"created_at":"2026-07-19T00:33:24.451129Z","pmid":"36092819","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":[]}