{"doi":"10.1093/bioinformatics/btt316","title":"Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool","abstract":"

Motivation

Biological analysis has shifted from identifying genes and transcripts to mapping these genes and transcripts to biological functions. The ENCODE Project has generated hundreds of ChIP-Seq experiments spanning multiple transcription factors and cell lines for public use, but tools for a biomedical scientist to analyze these data are either non-existent or tailored to narrow biological questions. We present the ENCODE ChIP-Seq Significance Tool, a flexible web application leveraging public ENCODE data to identify enriched transcription factors in a gene or transcript list for comparative analyses.

Implementation

The ENCODE ChIP-Seq Significance Tool is written in JavaScript on the client side and has been tested on Google Chrome, Apple Safari and Mozilla Firefox browsers. Server-side scripts are written in PHP and leverage R and a MySQL database. The tool is available at http://encodeqt.stanford.edu.

Contact

abutte@stanford.edu

Supplementary information

Supplementary material is available at Bioinformatics online.","journal":"Bioinformatics","year":2013,"id":6043,"datarank":4.15554247383066,"base_score":4.304065093204169,"endowment":4.304065093204169,"self_citation_contribution":0.6456097639806255,"citation_network_contribution":3.5099327098500344,"self_endowment_contribution":0.6456097639806255,"citer_contribution":3.5099327098500344,"corpus_percentile":null,"corpus_rank":null,"citation_count":73,"citer_count":67,"citers_with_citation_signal":58,"citers_with_endowment":58,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.0766,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2013-06-03","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":11850,"name":"BIN CHEN","orcid":"0000-0001-8858-874X","position":1,"is_corresponding":false},{"id":51,"name":"Atul Janardhan Butte","orcid":"0000-0002-7433-2740","position":2,"is_corresponding":false},{"id":57232,"name":"Raymond K. Auerbach","orcid":null,"position":0,"is_corresponding":true}],"reference_count":5,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","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":[]}