TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions
By Heonjong Han, Jae-Won Cho, Sang-Young Lee, Ayoung Yun, Hyojin Kim, D. Bae, Sunmo Yang, Chan Yeong Kim, Muyoung Lee, Eunbee Kim and 10 more. Nucleic Acids Res., 2017
1,732 citations recorded by the source corpus.
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.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/ba90ae48b30594b57a5ca7bfd37cae150458ecfa
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In Molecular Biology
Citations in the corpus
- Gene regulatory network inference in the era of single-cell multi-omics (2023, background): “Histori-cally, GRNs have been commonly assembled from experimentally validated regulation events compiled in databases 14–17 or inferred de novo from gene co-expression in bulk transcriptomics data 18–20 .”
- hTFtarget: A Comprehensive Database for Regulations of Human Transcription Factors and Their Targets (2019, neutral): “Although several resources, such as ReMap [9], CistromeDB [10], Factorbook [11], ChIPBase [12], and TRRUST [13], were conducted to display the relationships between mammalian TFs and their targets.”