The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
Motif-based analysis of large nucleotide data sets using MEME-ChIP
Open accessAbstract
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696
ChIP–seq: advantages and challenges of a maturing technology
Park, P. J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2641 · Cited by 2,217
A compendium of RNA-binding motifs for decoding gene regulation
Ray, D., Kazan, H., Cook, K. B., Weirauch, M. T., Najafabadi, H. S., Li, X., Gueroussov, S., Albu, M., Zheng, H., Yang, A., et al. (2013) · Nature · doi:10.1038/nature12311 · Cited by 1,480 · cited 2×
“MEME-ChIP’s motif databases include DNA and RNA motifs assayed by using in vitro approaches (e.g., SELEX 33 , protein binding microarray 18 , competitive RNA binding 21 ) and in vivo motifs (e.g. JASPAR 17 ).”
MethodHITS-CLIP yields genome-wide insights into brain alternative RNA processing
Licatalosi, D. D., Mele, A., Fak, J. J., Ule, J., Kayikci, M., Chi, S. W., Clark, T. A., Schweitzer, A. C., Blume, J. E., Wang, X., et al. (2008) · Nature · doi:10.1038/nature07488 · Cited by 1,352 · cited 2×
“CLIP-seq, also known as HITS-CLIP, screens for cross-linking sites between RBPs and RNA molecules via UV-cross-linking and immunoprecipitation 34,35 .”
BackgroundMethodA high-resolution map of the three-dimensional chromatin interactome in human cells
Jin, F., Li, Y., Dixon, J. R., Selvaraj, S., Ye, Z., Lee, A. Y., Yen, C.-A., Schmitt, A. D., Espinoza, C. A., & Ren, B. (2013) · Nature · doi:10.1038/nature12644 · Cited by 1,208
iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution
König, J., Zarnack, K., Rot, G., Curk, T., Kayikci, M., Zupan, B., Turner, D. J., Luscombe, N. M., & Ule, J. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1838 · Cited by 1,126
Hogan, D. J., Riordan, D. P., Gerber, A. P., Herschlag, D., & Brown, P. O. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060255 · Cited by 609
Cited by
m6A RNA methylation promotes XIST-mediated transcriptional repression
Patil, D. P., Chen, C.-K., Pickering, B. F., Chow, A., Jackson, C., Guttman, M., & Jaffrey, S. R. (2016) · Nature · doi:10.1038/nature19342 · Cited by 1,747
hTFtarget: A Comprehensive Database for Regulations of Human Transcription Factors and Their Targets
Zhang, Q., Liu, W., Zhang, H.-M., Xie, G.-Y., Miao, Y.-R., Xia, M., & Guo, A.-Y. (2020) · Genomics, Proteomics & Bioinformatics · doi:10.1016/j.gpb.2019.09.006 · Cited by 600
A Comprehensive Roadmap of Murine Spermatogenesis Defined by Single-Cell RNA-Seq
Green, C. D., Ma, Q., Manske, G. L., Shami, A. N., Zheng, X., Marini, S., Moritz, L., Sultan, C., Gurczynski, S. J., Moore, B. B., et al. (2018) · Developmental Cell · doi:10.1016/j.devcel.2018.07.025 · Cited by 521
Zong, W., Tang, N., Yang, J., Peng, L., Ma, S., Xu, Y., Li, G., & Xiong, L. (2016) · Plant Physiology · doi:10.1104/pp.16.00469 · Cited by 336
Conservation and innovation in the DUX4-family gene network
Whiddon, J. L., Langford, A. T., Wong, C.-J., Zhong, J. W., & Tapscott, S. J. (2017) · Nature Genetics · doi:10.1038/ng.3846 · Cited by 334
Metadata
- Authors
- Ma, W., Noble, W. S., & Bailey, T. L.
- Venue
- Nature Protocols
- Published
- 2014-05-22
- Volume
- 9
- Issue
- 6
- Pages
- 1428-1450
- ISSN
- 1750-2799 (ISSN-L)
- 1754-2189
- OpenAlex
- W2060445972
- Cited by
- 240
- References
- 8
- FWCI
- 6.33
- Type
- journal article
- Language
- en
- Open access
- green
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Motif-based analysis of large nucleotide data sets using MEME-ChIP. https://app.cochat.ai/papers/10.1038/nprot.2014.083
- The paper
- Ma, W., Noble, W. S., & Bailey, T. L. (2014). Motif-based analysis of large nucleotide data sets using MEME-ChIP. Nature Protocols. https://doi.org/10.1038/nprot.2014.083
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
