{"doi":"10.1101/036053","title":"RTFBSDB: an integrated framework for transcription factor binding site analysis","abstract":"<jats:title>Abstract</jats:title>\n                <jats:p>\n                  Transcription factors (TFs) regulate complex programs of gene transcription by binding to short DNA sequence motifs. Here we introduce\n                  <jats:italic>rtfbsdb</jats:italic>\n                  , a unified framework that integrates a database of more than 65,000 TF binding motifs with tools to easily and efficiently scan target genome sequences.\n                  <jats:italic>Rtfbsdb</jats:italic>\n                  clusters motifs with similar DNA sequence specificities and optionally integrates RNA-seq or PRO-seq data to restrict analyses to motifs recognized by TFs expressed in the cell type of interest. Our package allows common analyses to be performed rapidly in an integrated environment.\n                </jats:p>\n                <jats:p>\n                  <jats:bold>Availability:</jats:bold>\n                  <jats:italic>rtfbsdb</jats:italic>\n                  is available via github (\n                  <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" ext-link-type=\"uri\" xlink:href=\"https://github.com/Danko-Lab/rtfbsdb\">https://github.com/Danko-Lab/rtfbsdb</jats:ext-link>\n                  ).\n                </jats:p>","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":null,"id":588318,"datarank":0.20281537494842372,"base_score":1.0986122886681096,"endowment":1.0986122886681096,"self_citation_contribution":0.16479184330021646,"citation_network_contribution":0.038023531648207265,"self_endowment_contribution":0.16479184330021646,"citer_contribution":0.038023531648207265,"corpus_percentile":null,"corpus_rank":null,"citation_count":2,"citer_count":1,"citers_with_citation_signal":1,"citers_with_endowment":1,"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":41929,"name":"Andre L. Martins","orcid":null,"position":1,"is_corresponding":false},{"id":19579,"name":"Charles G. Danko","orcid":"0000-0002-1999-7125","position":2,"is_corresponding":false},{"id":6833,"name":"Zhong Wang","orcid":"0000-0002-6307-0458","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"RTFBSDB: an integrated framework for transcription factor binding site analysis","abstract":"Transcription factors (TFs) regulate complex programs of gene transcription by binding to short DNA sequence motifs. Here we introduce  rtfbsdb , a unified framework that integrates a database of more than 65,000 TF binding motifs with tools to easily and efficiently scan target genome sequences.  Rtfbsdb clusters motifs with similar DNA sequence specificities and optionally integrates RNA-seq or PRO-seq data to restrict analyses to motifs recognized by TFs expressed in the cell type of interest. Our package allows common analyses to be performed rapidly in an integrated environment.  Availability: rtfbsdb is available via github (  https://github.com/Danko-Lab/rtfbsdb ).","is_dataset_classified":null,"base_score":0.0,"endowment":0.0,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"26657633","pmcid":null,"openalex_id":null,"authors":[],"funders":[],"total_grants":0,"fwci":null,"citation_percentile":null,"influential_citations":0,"citation_trend":[],"oa_status":"green","license":"cc-by-nd","oa_locations":[{"url":"https://www.biorxiv.org/content/biorxiv/early/2016/01/05/036053.full.pdf","host_type":"repository"}],"fields_of_study":[],"mesh_terms":[],"keywords":[],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-20T08:45:22.935546Z","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":[]}