Identifying active transcriptional regulators (TRs) associating with cis-regulatory elements in the genome to regulate gene expression is a key task in gene regulation research. TR binding profiles from numerous public ChIP-seq data can be utilized for association analysis with query data for TR identification, as an alternative to DNA sequence motif analysis. However, integration of the massive ChIP-seq datasets has been a major challenge in such approaches. Here we present BARTweb, an interactive web server for identifying TRs whose genomic binding patterns associate with input genomic features, by leveraging over 13 000 public ChIP-seq datasets for human and mouse. Using an updated binding analysis for regulation of transcription (BART) algorithm, BARTweb can identify functional TRs that regulate a gene set, have a binding profile correlated with a ChIP-seq profile or are enriched in a genomic region set, without a priori information of the cell type. BARTweb can be a useful web server for performing functional analysis of gene regulation. BARTweb is freely available at http://bartweb.org and the source code is available at https://github.com/zanglab/bart2.
© The Author(s) 2021. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.