{"doi":"10.1016/j.celrep.2020.108064","title":"Transite: A Computational Motif-Based Analysis Platform That Identifies RNA-Binding Proteins Modulating Changes in Gene Expression","abstract":"RNA-binding proteins (RBPs) play critical roles in regulating gene expression by modulating splicing, RNA stability, and protein translation. Stimulus-induced alterations in RBP function contribute to global changes in gene expression, but identifying which RBPs are responsible for the observed changes remains an unmet need. Here, we present Transite, a computational approach that systematically infers RBPs influencing gene expression through changes in RNA stability and degradation. As a proof of principle, we apply Transite to RNA expression data from human patients with non-small-cell lung cancer whose tumors were sampled at diagnosis or after recurrence following treatment with platinum-based chemotherapy. Transite implicates known RBP regulators of the DNA damage response and identifies hnRNPC as a new modulator of chemotherapeutic resistance, which we subsequently validated experimentally. Transite serves as a framework for the identification of RBPs that drive cell-state transitions and adds additional value to the vast collection of publicly available gene expression datasets.","journal":"Cell Reports","year":2020,"id":60810,"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":60,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9591,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":321032,"name":"Molly A. Bird","orcid":"0000-0001-7650-9610","position":1,"is_corresponding":false},{"id":321033,"name":"Shohreh Varmeh","orcid":"0000-0002-7058-1184","position":2,"is_corresponding":false},{"id":321034,"name":"Erika D. Handly","orcid":"0000-0001-8788-3050","position":3,"is_corresponding":false},{"id":321035,"name":"Anna Gattinger","orcid":"0000-0001-7094-9279","position":4,"is_corresponding":false},{"id":321036,"name":"Thomas Bernwinkler","orcid":"0000-0002-5632-072X","position":5,"is_corresponding":false},{"id":321037,"name":"Daniel A. Anderson","orcid":"0000-0001-9655-323X","position":6,"is_corresponding":false},{"id":321038,"name":"Andreas Heinzel","orcid":"0000-0002-8447-1795","position":7,"is_corresponding":false},{"id":231599,"name":"Brian A. Joughin","orcid":"0000-0003-1022-9450","position":8,"is_corresponding":false},{"id":259261,"name":"Yi Wen Kong","orcid":"0000-0002-4223-971X","position":9,"is_corresponding":false},{"id":94620,"name":"Ian G. Cannell","orcid":"0000-0001-5832-9210","position":10,"is_corresponding":false},{"id":201960,"name":"Michael B Yaffe","orcid":"0000-0002-9547-3251","position":11,"is_corresponding":false},{"id":321031,"name":"Konstantin Krismer","orcid":"0000-0001-8994-3416","position":0,"is_corresponding":true}],"reference_count":75,"raw_metadata":null,"created_at":"2026-07-18T21:09:05.493770Z","pmid":"32846122","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":[]}