UniBind

Transcription factor-DNA interaction database across nine species, with quality-tiered binding site predictions from uniformly processed ChIP-seq data.

Overview

UniBind is a database and web portal providing access to direct transcription factor (TF)–DNA interaction data across nine species. It is hosted by the University of Oslo and ELIXIR Norway, and is intended to support researchers working in gene regulation and transcription. The portal offers a map of transcription factor binding sites (TFBSs) derived from uniform processing of thousands of ChIP-seq datasets using the ChIP-eat software pipeline.

Datasets in UniBind are divided into two quality-tiered collections: robust and permissive. Classification is based on two quality control metrics — the similarity of the DAMO-optimized TF binding motif to the expected canonical motif, and the enrichment of TFBSs around ChIP-seq peak summits. Datasets satisfying both criteria are placed in the robust collection; all others are classified as permissive.

Key Features

Covers TF binding site data across nine species, including human, mouse, and rat
Incorporates thousands of ChIP-seq datasets, all uniformly processed for consistency and comparability
Provides robust and permissive dataset collections, allowing users to select the confidence level appropriate for their analysis
Binding site calls are validated against canonical motifs and peak summit enrichment to support high-confidence predictions
Uses the ChIP-eat pipeline to standardize processing and ensure reproducibility across all datasets
All data are freely available through the web portal and can be downloaded in bulk for use in external analyses

Typical Workflow

Browse available species and transcription factors through the UniBind portal
Select a species and TF of interest to view the corresponding binding site predictions
Choose between the robust or permissive collection depending on the confidence requirements of the analysis
Download the relevant datasets for integration with genomic analysis workflows

UniBind is an open-access resource. The underlying ChIP-eat software used for dataset processing is also publicly available, supporting transparency and reproducibility in TF binding site analysis.