{"doi":"10.1101/gr.4140006","title":"Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques","abstract":"<jats:p>Fields such as genomics and systems biology are built on the synergism between computational and experimental techniques. This type of synergism is especially important in accomplishing goals like identifying all functional transcription factor binding sites in vertebrate genomes. Precise detection of these elements is a prerequisite to deciphering the complex regulatory networks that direct tissue specific and lineage specific patterns of gene expression. This review summarizes approaches for in silico, in vitro, and in vivo identification of transcription factor binding sites. A variety of techniques useful for localized- and high-throughput analyses are discussed here, with emphasis on aspects of data generation and verification.</jats:p>","journal":"Genome Research","year":2006,"id":45372,"datarank":9.25792341785496,"base_score":5.393627546352361,"endowment":5.393627546352361,"self_citation_contribution":0.8090441319528543,"citation_network_contribution":8.448879285902105,"self_endowment_contribution":0.8090441319528543,"citer_contribution":8.448879285902105,"corpus_percentile":null,"corpus_rank":null,"citation_count":219,"citer_count":200,"citers_with_citation_signal":169,"citers_with_endowment":169,"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":88614,"name":"Victor X. Jin","orcid":"0000-0002-8765-3471","position":1,"is_corresponding":false},{"id":20034,"name":"Peggy J. Farnham","orcid":"0000-0003-4469-7914","position":2,"is_corresponding":false},{"id":14377,"name":"Steven J.M. Jones","orcid":"0000-0003-3394-2208","position":3,"is_corresponding":false},{"id":89052,"name":"Laura Elnitski","orcid":"0000-0003-1065-019X","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":5.393627546352361,"endowment":5.393627546352361,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"17053094","pmcid":null,"openalex_id":"https://openalex.org/W2112717966","authors":[],"funders":[{"funder_name":"NHGRI NIH HHS","grant_id":"HG003129","title":null},{"funder_name":"NCI NIH HHS","grant_id":"CA45240","title":null},{"funder_name":"NIDDK NIH HHS","grant_id":"DK167889","title":null},{"funder_name":"Intramural NIH HHS","grant_id":"","title":null},{"funder_name":"Intramural NIH HHS","grant_id":"","title":null}],"total_grants":5,"fwci":null,"citation_percentile":null,"influential_citations":18,"citation_trend":[{"year":2012,"count":19},{"year":2013,"count":15},{"year":2014,"count":12},{"year":2015,"count":7},{"year":2016,"count":9},{"year":2017,"count":3},{"year":2018,"count":5},{"year":2019,"count":8},{"year":2020,"count":6},{"year":2021,"count":5},{"year":2022,"count":4},{"year":2023,"count":3},{"year":2024,"count":3}],"oa_status":"hybrid","license":"other-oa","oa_locations":[{"url":"https://genome.cshlp.org/content/16/12/1455.full.pdf","host_type":"journal"},{"url":"https://genome.cshlp.org/content/16/12/1455.full.pdf","host_type":"HYBRID"},{"url":"https://genome.cshlp.org/content/16/12/1455.full.pdf","host_type":"publisher"},{"url":"https://syndication.highwire.org/content/doi/10.1101/gr.4140006","host_type":"publisher"},{"url":"https://doi.org/10.1101/gr.4140006","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/17053094","host_type":"repository"},{"url":"http://genome.cshlp.org/cgi/content/short/16/12/1455","host_type":"repository"}],"fields_of_study":["Genomics and Chromatin Dynamics","Animal Genetics and Reproduction","Single-cell and spatial transcriptomics","Biology","Medicine","Computer Science","Animals","Binding Sites","Chromatin Immunoprecipitation","Computational Biology","Databases, Genetic","Electrophoretic Mobility Shift Assay","Humans","Mammals","Oligonucleotide Array Sequence Analysis","Protein Binding","Transcription Factors"],"mesh_terms":["Animals","Binding Sites","Humans","Mammals","Protein Binding","Transcription Factors","Computational Biology","Oligonucleotide Array Sequence Analysis","Electrophoretic Mobility Shift Assay","Databases, Genetic","Chromatin Immunoprecipitation"],"keywords":["Biology","In silico","Computational biology","Transcription factor","DNA binding site","Genomics","Genome","Genetics","Gene","Gene expression","Promoter"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-03T01:09:06.383033Z","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":[]}