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Motif-based analysis of large nucleotide data sets using MEME-ChIP

Nature Protocols volume 9, pages 1428–1450 (2014)Cite this article

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Abstract

MEME-ChIP is a web-based tool for analyzing motifs in large DNA or RNA data sets. It can analyze peak regions identified by ChIP-seq, cross-linking sites identified by CLIP-seq and related assays, as well as sets of genomic regions selected using other criteria. MEME-ChIP performs de novo motif discovery, motif enrichment analysis, motif location analysis and motif clustering, providing a comprehensive picture of the DNA or RNA motifs that are enriched in the input sequences. MEME-ChIP performs two complementary types of de novo motif discovery: weight matrix–based discovery for high accuracy; and word-based discovery for high sensitivity. Motif enrichment analysis using DNA or RNA motifs from human, mouse, worm, fly and other model organisms provides even greater sensitivity. MEME-ChIP's interactive HTML output groups and aligns significant motifs to ease interpretation. This protocol takes less than 3 h, and it provides motif discovery approaches that are distinct and complementary to other online methods.

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Figure 1: MEME-ChIP submission form.
Figure 2: Universal options (expanded).
Figure 3: MEME options (expanded).
Figure 4: DREME options (expanded).
Figure 5: CentriMo options (expanded).
Figure 6: Job verification page.
Figure 7: MEME-ChIP report (top).
Figure 8: MEME-ChIP report (PROGRAMS).
Figure 9: MEME-ChIP report (INPUT FILES and command line).
Figure 10: MEME-ChIP report (MOTIFS).
Figure 11: MEME-ChIP report (top motif group expanded).
Figure 12: JASPAR Gata1 motif.
Figure 13: Tomtom analysis of MEME Gata1 motif (two most similar known motifs).
Figure 14: CentriMo analysis of GATA1 ChIP-seq peaks (top 15 most centrally enriched motifs).
Figure 15: CentriMo analysis reveals peak-calling artifacts.
Figure 16: MEME-ChIP report (fourth motif group expanded).
Figure 17: Tomtom analysis of DREME motifs.
Figure 18: Puf3p MEME-ChIP report (top).
Figure 19: Puf3p MEME-ChIP report (top motif group expanded).
Figure 20: CentriMo analysis of Puf3p PAR-CLIP cross-linking regions (top three most locally enriched motifs).
Figure 21: Puf3p MEME-ChIP report (top four motifs).

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Acknowledgements

This work was supported by the US National Institutes of Health awards R01 RR021692, R01 GM103544 and R01 GM098039.

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Authors and Affiliations

  1. Department of Genome Sciences, University of Washington, Seattle, Washington, USA

    Wenxiu Ma & William S Noble

  2. Department of Computer Science and Engineering, University of Washington, Seattle, Washington, USA

    William S Noble

  3. Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia

    Timothy L Bailey

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Contributions

W.M. and W.S.N. wrote the initial draft. T.L.B. conceived the study cases, wrote the anticipated results section and wrote the second draft. W.M. and T.L.B. verified the study cases. W.S.N., W.M. and T.L.B. edited the final manuscript.

Corresponding author

Correspondence to Timothy L Bailey.

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Ma, W., Noble, W. & Bailey, T. Motif-based analysis of large nucleotide data sets using MEME-ChIP. Nat Protoc 9, 1428–1450 (2014). https://doi.org/10.1038/nprot.2014.083

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