{"doi":"10.1016/j.celrep.2020.108029","title":"Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types","abstract":"Characterizing the tissue-specific binding sites of transcription factors (TFs) is essential to reconstruct gene regulatory networks and predict functions for non-coding genetic variation. DNase-seq footprinting enables the prediction of genome-wide binding sites for hundreds of TFs simultaneously. Despite the public availability of high-quality DNase-seq data from hundreds of samples, a comprehensive, up-to-date resource for the locations of genomic footprints is lacking. Here, we develop a scalable footprinting workflow using two state-of-the-art algorithms: Wellington and HINT. We apply our workflow to detect footprints in 192 ENCODE DNase-seq experiments and predict the genomic occupancy of 1,515 human TFs in 27 human tissues. We validate that these footprints overlap true-positive TF binding sites from ChIP-seq. We demonstrate that the locations, depth, and tissue specificity of footprints predict effects of genetic variants on gene expression and capture a substantial proportion of genetic risk for complex traits.","journal":"Cell Reports","year":2020,"id":93854,"datarank":1.2474420463063594,"base_score":3.6888794541139363,"endowment":3.6888794541139363,"self_citation_contribution":0.5533319181170905,"citation_network_contribution":0.6941101281892689,"self_endowment_contribution":0.5533319181170905,"citer_contribution":0.6941101281892689,"corpus_percentile":83.5228591320492,"corpus_rank":2131,"citation_count":39,"citer_count":29,"citers_with_citation_signal":24,"citers_with_endowment":24,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.8953,"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":468102,"name":"Alex M. Casella","orcid":"0000-0001-6873-7867","position":1,"is_corresponding":false},{"id":335541,"name":"Segun Jung","orcid":null,"position":2,"is_corresponding":false},{"id":468761,"name":"Matthew A. Richards","orcid":null,"position":3,"is_corresponding":false},{"id":468103,"name":"Álex Rodríguez","orcid":"0000-0002-0213-6695","position":4,"is_corresponding":false},{"id":468104,"name":"Paul Shannon","orcid":"0009-0003-6641-3115","position":5,"is_corresponding":false},{"id":468105,"name":"Rory Donovan-Maiye","orcid":"0000-0001-8080-9771","position":6,"is_corresponding":false},{"id":234819,"name":"Ben Heavner","orcid":"0000-0003-2898-9044","position":7,"is_corresponding":false},{"id":49292,"name":"Kyle Chard","orcid":"0000-0002-7370-4805","position":8,"is_corresponding":false},{"id":468762,"name":"Yukai Xiao","orcid":null,"position":9,"is_corresponding":false},{"id":6464,"name":"Gustavo Glusman","orcid":"0000-0001-8060-5955","position":10,"is_corresponding":false},{"id":776,"name":"Nilüfer Ertekin‐Taner","orcid":"0000-0003-4436-8889","position":11,"is_corresponding":false},{"id":107091,"name":"Todd E. Golde","orcid":"0000-0003-1867-7071","position":12,"is_corresponding":false},{"id":51713,"name":"Arthur W. Toga","orcid":"0000-0001-7902-3755","position":13,"is_corresponding":false},{"id":32944,"name":"Leroy Hood","orcid":"0000-0001-7158-3678","position":14,"is_corresponding":false},{"id":54506,"name":"John D. Van Horn","orcid":"0000-0003-1537-0816","position":15,"is_corresponding":false},{"id":70342,"name":"Carl Kesselman","orcid":"0000-0003-0917-1562","position":16,"is_corresponding":false},{"id":40513,"name":"Ian Foster","orcid":"0000-0003-2129-5269","position":17,"is_corresponding":false},{"id":64667,"name":"Ravi Madduri","orcid":"0000-0003-2130-2887","position":18,"is_corresponding":false},{"id":33002,"name":"Nathan D. Price","orcid":"0000-0002-4157-0267","position":19,"is_corresponding":false},{"id":235850,"name":"Seth A. Ament","orcid":"0000-0001-6443-7509","position":20,"is_corresponding":false},{"id":232914,"name":"Cory C. Funk","orcid":"0000-0002-5229-9011","position":0,"is_corresponding":true}],"reference_count":62,"raw_metadata":null,"created_at":"2026-07-18T22:31:34.149524Z","pmid":"32814038","pmcid":"PMC7462736","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":[]}