{"doi":"10.1371/journal.pone.0222459","title":"uORF-Tools—Workflow for the determination of translation-regulatory upstream open reading frames","abstract":null,"journal":"PLOS ONE","year":2019,"id":623900,"datarank":0.6351650115577221,"base_score":2.4849066497880004,"endowment":2.4849066497880004,"self_citation_contribution":0.37273599746820013,"citation_network_contribution":0.2624290140895219,"self_endowment_contribution":0.37273599746820013,"citer_contribution":0.2624290140895219,"corpus_percentile":null,"corpus_rank":null,"citation_count":11,"citer_count":10,"citers_with_citation_signal":6,"citers_with_endowment":6,"datacite_reuse_total":0,"is_dataset":false,"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":1612586,"name":"Florian Eggenhofer","orcid":null,"position":1,"is_corresponding":false},{"id":1612587,"name":"Rick Gelhausen","orcid":null,"position":2,"is_corresponding":false},{"id":30115,"name":"Björn Grüning","orcid":"0000-0002-3079-6586","position":3,"is_corresponding":false},{"id":670940,"name":"Kathi Zarnack","orcid":"0000-0003-3527-3378","position":4,"is_corresponding":false},{"id":407131,"name":"Bernhard Brüne","orcid":"0000-0001-8237-2841","position":5,"is_corresponding":false},{"id":92482,"name":"Rolf Backofen","orcid":"0000-0001-8231-3323","position":6,"is_corresponding":false},{"id":1612592,"name":"Tobias Schmid","orcid":"0000-0002-1952-5259","position":7,"is_corresponding":false},{"id":1612585,"name":"Anica Scholz","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"uORF-Tools—Workflow for the determination of translation-regulatory upstream open reading frames","abstract":"Ribosome profiling (ribo-seq) provides a means to analyze active translation by determining ribosome occupancy in a transcriptome-wide manner. The vast majority of ribosome protected fragments (RPFs) resides within the protein-coding sequence of mRNAs. However, commonly reads are also found within the transcript leader sequence (TLS) (aka 5' untranslated region) preceding the main open reading frame (ORF), indicating the translation of regulatory upstream ORFs (uORFs). Here, we present a workflow for the identification of translation-regulatory uORFs. Specifically, uORF-Tools uses Ribo-TISH to identify uORFs within a given dataset and generates a uORF annotation file. In addition, a comprehensive human uORF annotation file, based on 35 ribo-seq files, is provided, which can serve as an alternative input file for the workflow. To assess the translation-regulatory activity of the uORFs, stimulus-induced changes in the ratio of the RPFs residing in the main ORFs relative to those found in the associated uORFs are determined. The resulting output file allows for the easy identification of candidate uORFs, which have translation-inhibitory effects on their associated main ORFs. uORF-Tools is available as a free and open Snakemake workflow at https://github.com/Biochemistry1-FFM/uORF-Tools. It is easily installed and all necessary tools are provided in a version-controlled manner, which also ensures lasting usability. uORF-Tools is designed for intuitive use and requires only limited computing times and resources.","is_dataset_classified":null,"base_score":2.4849066497880004,"endowment":2.4849066497880004,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"31513641","pmcid":"PMC6742470","openalex_id":"https://openalex.org/W2973179166","authors":[],"funders":[{"funder_name":"Deutsche Forschungsgemeinschaft","grant_id":"SCHM2663/3","title":null},{"funder_name":"Deutsche Forschungsgemeinschaft","grant_id":"INST 37/935-1","title":null},{"funder_name":"Deutsche Forschungsgemeinschaft","grant_id":"BA 2168/21-1","title":null},{"funder_name":"Deutsche Forschungsgemeinschaft","grant_id":"unidentified","title":"unidentified"},{"funder_name":"Deutsche Forschungsgemeinschaft","grant_id":"313752925/SPP 2002","title":"Small Proteins in Prokaryotes, an Unexplored World"},{"funder_name":"Stiftung Polytechnische Gesellschaft Frankfurt","grant_id":"","title":null}],"total_grants":6,"fwci":0.5314,"citation_percentile":0.63221971,"influential_citations":0,"citation_trend":[{"year":2019,"count":1},{"year":2020,"count":3},{"year":2021,"count":2},{"year":2022,"count":1},{"year":2023,"count":2},{"year":2025,"count":1},{"year":2026,"count":1}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0222459&type=printable","host_type":"journal"},{"url":"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0222459&type=printable","host_type":"publisher"},{"url":"http://dx.plos.org/10.1371/journal.pone.0222459","host_type":"publisher"},{"url":"https://doi.org/10.1371/journal.pone.0222459","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/31513641","host_type":"repository"},{"url":"https://doaj.org/article/49a2a1380fb540198a48dc14691e8913","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6742470","host_type":"repository"},{"url":"https://figshare.com/articles/dataset/_i_uORF-Tools_i_Workflow_for_the_determination_of_translation-regulatory_upstream_open_reading_frames/9818753","host_type":"repository"},{"url":"https://freidok.uni-freiburg.de/data/267777","host_type":"repository"},{"url":"http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/51078","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC6742470","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC6742470?pdf=render","host_type":"Europe_PMC"},{"url":"https://doi.org/10.1101/415018","host_type":""},{"url":"http://dx.doi.org/10.1371/journal.pone.0222459","host_type":""},{"url":"https://dx.doi.org/10.1101/415018","host_type":""},{"url":"https://dx.doi.org/10.1371/journal.pone.0222459","host_type":""},{"url":"http://dx.doi.org/10.1101/415018","host_type":""},{"url":"https://doi.org/https://doi.org/10.1371/journal.pone.0222459","host_type":""}],"fields_of_study":["RNA and protein synthesis mechanisms","RNA modifications and cancer","RNA Research and Splicing","0301 basic medicine","0206 medical engineering","02 engineering and technology","03 medical and health sciences","0302 clinical medicine","5' Untranslated Regions","Gene Expression Profiling","Gene Expression Regulation","Humans","Open Reading Frames","Protein Biosynthesis","Protein Processing, Post-Translational","RNA, Messenger","Ribosomes","Software","Workflow"],"mesh_terms":["Gene Expression Regulation","Humans","Protein Processing, Post-Translational","Ribosomes","RNA, Messenger","Software","Protein Biosynthesis","Open Reading Frames","5' Untranslated Regions","Gene Expression Profiling","Workflow"],"keywords":["Upstream open reading frame","ORFS","Open reading frame","Ribosome profiling","Five prime untranslated region","Workflow","Computer science","Annotation","Translation (biology)","Computational biology","Biology","Genetics","Database","Messenger RNA","Gene","Peptide sequence","ddc:610","020","Science","Gene Expression Profiling","Q","R","610","Open Reading Frames","Gene Expression Regulation","Protein Biosynthesis","Medicine","Humans","RNA, Messenger","5' Untranslated Regions","Protein Processing, Post-Translational","Ribosomes","Software","Research Article"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Quality Education"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"geo"},{"name":"doi"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-04T01:52:38.017810Z","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":[]}