TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions

TLDR

Transcription factors are key trans‑acting regulators, and mapping their target interactions is essential for deciphering the regulatory networks that underlie complex traits like human diseases. The study introduces TRRUST v2, an expanded and more comprehensive human TF‑target interaction database, along with a new web tool for prioritizing key transcription factors in disease contexts. TRRUST v2 was built by sentence‑based text mining and manual curation, and its web interface was enhanced to allow users to prioritize key transcription factors based on sets of responsive genes. TRRUST v2 now contains 8,444 human and 6,552 mouse TF‑target interactions, covering 800 and 828 transcription factors, and is more comprehensive and less biased than other databases.

Abstract

Transcription factors (TFs) are major trans-acting factors in transcriptional regulation. Therefore, elucidating TF-target interactions is a key step toward understanding the regulatory circuitry underlying complex traits such as human diseases. We previously published a reference TF-target interaction database for humans-TRRUST (Transcriptional Regulatory Relationships Unraveled by Sentence-based Text mining)-which was constructed using sentence-based text mining, followed by manual curation. Here, we present TRRUST v2 (www.grnpedia.org/trrust) with a significant improvement from the previous version, including a significantly increased size of the database consisting of 8444 regulatory interactions for 800 TFs in humans. More importantly, TRRUST v2 also contains a database for TF-target interactions in mice, including 6552 TF-target interactions for 828 mouse TFs. TRRUST v2 is also substantially more comprehensive and less biased than other TF-target interaction databases. We also improved the web interface, which now enables prioritization of key TFs for a physiological condition depicted by a set of user-input transcriptional responsive genes. With the significant expansion in the database size and inclusion of the new web tool for TF prioritization, we believe that TRRUST v2 will be a versatile database for the study of the transcriptional regulation involved in human diseases.