The DOI matches its Crossref record; 11 of the 11 references it cites were found in a registry or an index.
Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity
Open accessAbstract
Transcription factor (TF) DNA sequence preferences direct their regulatory activity, but are currently known for only ∼1% of eukaryotic TFs. Broadly sampling DNA-binding domain (DBD) types from multiple eukaryotic clades, we determined DNA sequence preferences for >1,000 TFs encompassing 54 different DBD classes from 131 diverse eukaryotes. We find that closely related DBDs almost always have very similar DNA sequence preferences, enabling inference of motifs for ∼34% of the ∼170,000 known or predicted eukaryotic TFs. Sequences matching both measured and inferred motifs are enriched in chromatin immunoprecipitation sequencing (ChIP-seq) peaks and upstream of transcription start sites in diverse eukaryotic lineages. SNPs defining expression quantitative trait loci in Arabidopsis promoters are also enriched for predicted TF binding sites. Importantly, our motif "library" can be used to identify specific TFs whose binding may be altered by human disease risk alleles. These data present a powerful resource for mapping transcriptional networks across eukaryotes.
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Self-citationA compendium of RNA-binding motifs for decoding gene regulation
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Self-citationVariation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences
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Self-citationEvaluation of methods for modeling transcription factor sequence specificity
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Recovering Gene Interactions from Single-Cell Data Using Data Diffusion
van Dijk, D., Sharma, R., Nainys, J., Yim, K., Kathail, P., Carr, A. J., Burdziak, C., Moon, K. R., Chaffer, C. L., Pattabiraman, D., et al. (2018) · Cell · doi:10.1016/j.cell.2018.05.061 · Cited by 1,829
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Metadata
- Authors
- Weirauch, M. T., Yang, A., Albu, M., Cote, A. G., Montenegro-Montero, A., Drewe, P., Najafabadi, H. S., Lambert, S. A., Mann, I., Cook, K., Zheng, H., Goity, A., van Bakel, H., Lozano, J.-C., Galli, M., Lewsey, M. G., Huang, E., Mukherjee, T., Chen, X., Reece-Hoyes, J. S., Govindarajan, S., Shaulsky, G., Walhout, A. J. M., Bouget, F.-Y., Ratsch, G., Larrondo, L. F., Ecker, J. R., & Hughes, T. R.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2014-09
- Volume
- 158
- Issue
- 6
- Pages
- 1431-1443
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W2033169664
- Cited by
- 1,785
- References
- 11
- FWCI
- 33.58
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- The paper
- Weirauch, M. T., Yang, A., Albu, M., Cote, A. G., Montenegro-Montero, A., Drewe, P., Najafabadi, H. S., Lambert, S. A., Mann, I., Cook, K., Zheng, H., Goity, A., van Bakel, H., Lozano, J.-C., Galli, M., Lewsey, M. G., Huang, E., Mukherjee, T., Chen, X., . . . Hughes, T. R. (2014). Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity. Cell. https://doi.org/10.1016/j.cell.2014.08.009
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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