The DOI matches its Crossref record; 31 of the 31 references it cites were found in a registry or an index.
DREME: motif discovery in transcription factor ChIP-seq data
Open accessAbstract
Motivation: Transcription factor (TF) ChIP-seq datasets have particular characteristics that provide unique challenges and opportunities for motif discovery. Most existing motif discovery algorithms do not scale well to such large datasets, or fail to report many motifs associated with cofactors of the ChIP-ed TF. Results: We present DREME, a motif discovery algorithm specifically designed to find the short, core DNA-binding motifs of eukaryotic TFs, and optimized to analyze very large ChIP-seq datasets in minutes. Using DREME, we discover the binding motifs of the the ChIP-ed TF and many cofactors in mouse ES cell (mESC), mouse erythrocyte and human cell line ChIP-seq datasets. For example, in mESC ChIP-seq data for the TF Esrrb, we discover the binding motifs for eight cofactor TFs important in the maintenance of pluripotency. Several other commonly used algorithms find at most two cofactor motifs in this same dataset. DREME can also perform discriminative motif discovery, and we use this feature to provide evidence that Sox2 and Oct4 do not bind in mES cells as an obligate heterodimer. DREME is much faster than many commonly used algorithms, scales linearly in dataset size, finds multiple, non-redundant motifs and reports a reliable measure of statistical significance for each motif found. DREME is available as part of the MEME Suite of motif-based sequence analysis tools (http://meme.nbcr.net). Contact: t.bailey@uq.edu.au Supplementary information: Supplementary data are available at Bioinformatics online.
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TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes
Matys, V. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj143 · Cited by 2,166
Quantifying similarity between motifs
Gupta, S., Stamatoyannopoulos, J. A., Bailey, T. L., & Noble, W. S. (2007) · Genome Biology · doi:10.1186/gb-2007-8-2-r24 · Cited by 2,058
Self-citationJASPAR: an open-access database for eukaryotic transcription factor binding profiles
Sandelin, A. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh012 · Cited by 1,790
A census of human transcription factors: function, expression and evolution
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DNA binding sites: representation and discovery
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Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells
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The value of prior knowledge in discovering motifs with MEME.
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Soufi, A., Garcia, M. F., Jaroszewicz, A., Osman, N., Pellegrini, M., & Zaret, K. S. (2015) · Cell · doi:10.1016/j.cell.2015.03.017 · Cited by 780
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STREME: accurate and versatile sequence motif discovery
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Self-citationDirect promoter repression by BCL11A controls the fetal to adult hemoglobin switch
Liu, N., Hargreaves, V. V., Zhu, Q., Kurland, J. V., Hong, J., Kim, W., Sher, F., Macias-Trevino, C., Rogers, J. M., Kurita, R., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.016 · Cited by 478
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Metadata
- Authors
- Bailey, T. L.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-05-04
- Volume
- 27
- Issue
- 12
- Pages
- 1653-1659
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2097175728
- Cited by
- 1,044
- References
- 31
- FWCI
- 16.34
- Type
- journal article
- Language
- en
- Open access
- hybrid
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