The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions
Open accessAbstract
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.
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Cites
An atlas of combinatorial transcriptional regulation in mouse and man
Ravasi, T., Suzuki, H., Cannistraci, C. V., Katayama, S., Bajic, V. B., Tan, K., Akalin, A., Schmeier, S., Kanamori-Katayama, M., Bertin, N., et al. (2010) · Cell · doi:10.1016/j.cell.2010.01.044 · Cited by 715
TRRUST: a reference database of human transcriptional regulatory interactions
Han, H., Shim, H., Shin, D., Shim, J. E., Ko, Y., Shin, J., Kim, H., Cho, A., Kim, E., Lee, T., et al. (2015) · Scientific Reports · doi:10.1038/srep11432 · Cited by 462
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ChEA3: transcription factor enrichment analysis by orthogonal omics integration
Keenan, A. B., Torre, D., Lachmann, A., Leong, A. K., Wojciechowicz, M. L., Utti, V., Jagodnik, K. M., Kropiwnicki, E., Wang, Z., & Ma’ayan, A. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz446 · Cited by 1,136
Benchmark and integration of resources for the estimation of human transcription factor activities
Garcia-Alonso, L., Holland, C. H., Ibrahim, M. M., Turei, D., & Saez-Rodriguez, J. (2019) · Genome Research · doi:10.1101/gr.240663.118 · Cited by 1,122
Spatially organized multicellular immune hubs in human colorectal cancer
Pelka, K., Hofree, M., Chen, J. H., Sarkizova, S., Pirl, J. D., Jorgji, V., Bejnood, A., Dionne, D., Ge, W. H., Xu, K. H., et al. (2021) · Cell · doi:10.1016/j.cell.2021.08.003 · Cited by 874
Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data
Pratapa, A., Jalihal, A. P., Law, J. N., Bharadwaj, A., & Murali, T. M. (2020) · Nature Methods · doi:10.1038/s41592-019-0690-6 · Cited by 792
Mitochondrial stress is relayed to the cytosol by an OMA1–DELE1–HRI pathway
Guo, X., Aviles, G., Liu, Y., Tian, R., Unger, B. A., Lin, Y.-H. T., Wiita, A. P., Xu, K., Correia, M. A., & Kampmann, M. (2020) · Nature · doi:10.1038/s41586-020-2078-2 · Cited by 674
Metadata
- Authors
- Han, H., Cho, J.-W., Lee, S., Yun, A., Kim, H., Bae, D., Yang, S., Kim, C. Y., Lee, M., Kim, E., Lee, S., Kang, B., Jeong, D., Kim, Y., Jeon, H.-N., Jung, H., Nam, S., Chung, M., Kim, J.-H., & Lee, I.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-10-26
- Volume
- 46
- Issue
- D1
- Pages
- D380-D386
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2782454362
- Cited by
- 1,973
- References
- 2
- FWCI
- 28.92
- Type
- journal article
- Language
- en
- Open access
- gold
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- Han, H., Cho, J.-W., Lee, S., Yun, A., Kim, H., Bae, D., Yang, S., Kim, C. Y., Lee, M., Kim, E., Lee, S., Kang, B., Jeong, D., Kim, Y., Jeon, H.-N., Jung, H., Nam, S., Chung, M., Kim, J.-H., & Lee, I. (2018). TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions. Nucleic Acids Research. https://doi.org/10.1093/nar/gkx1013
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