MEME-ChIP protocols

View MEME-ChIP computational protocol

MEME-ChIP statistics

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chevron_left Motif enrichment analysis De novo motif discovery chevron_right
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MEME-ChIP specifications


Unique identifier OMICS_08098
Interface Web user interface
Restrictions to use None
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Timothy L Bailey <>

Publications for MEME-ChIP

MEME-ChIP in pipelines

PMCID: 5429095
PMID: 28395144
DOI: 10.7554/eLife.22194.055

[…] and chromatin states with the different genomic features, as well as to identify the nearest tss for each of the activated enhancer elements., de novo motif enrichment analyses were performed using meme-chip against jaspar core and uniprobe mouse databases (-meme-minw 6, -meme-maxw 15, meme-nmotifs 20, -dreme-e 0.05, -meme-mod zoops) (rrid:scr_001783) (). each motif was renamed according […]

PMCID: 5449609
PMID: 28334823
DOI: 10.1093/nar/gkx131

[…] h3.y-mutants. statistical testing of observed differences was done using wilcoxon-signed-rank test. de novo discovery of enriched motifs within sites with reduced h3.y binding was done with meme-chip (). coverage vectors were produced using deeptools bamcoverage function. similarly, deeptools was used for representation of chip-seq coverage across peak intervals as heat maps (). bigwig […]

PMCID: 5479651
PMID: 28691095
DOI: 10.1126/sciadv.1700191

[…] index and statistical tests that aim to identify spatial correlations between the two sets of genome features.j(a,b)=|a∩b||a∪b|, dna sequence motifs associated with cts and cfts were mined using meme-chip with the default settings (). the correlation of chip-seq peaks, after peak calling, was analyzed by bedtools jaccard. jaccard statistics measures the similarity of all 32 chip-seq peak […]

PMCID: 5482983
PMID: 28455373
DOI: 10.1242/dev.143479

[…] were analyzed using galaxy (), and the genomic spans given in bed format were converted to fasta files using the ucsc table browser () in order to be analyzed for sequence motif enrichment by meme-chip (). to compare human peak data with mouse data, human bed file data were transferred onto the mouse genome coordinates using the liftover tool of the ucsc genome browser. association […]

PMCID: 5561104
PMID: 28819152
DOI: 10.1038/s41598-017-08754-9

[…] significantly enriched for both the binomial and the hyper-geometric by a p-value lower than 0.05 were considered., prediction of tf binding motifs was performed using the centrimo algorithm of the meme-chip pipeline v.4.9.1 in default settings. a genomic region of +/−100 bp focused on each binding sites center was considered for this analysis., the normalization of chip signal profiles […]

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MEME-ChIP in publications

PMCID: 5943456
PMID: 29743479
DOI: 10.1038/s41467-018-04283-9

[…] (logfc and logfdr) were used to visualise differentially accessible regions in ris (red) and nis (purple) compared to growing cells in the comparisons indicated. plots were generated using ggplot2., meme-chip suite (version 4.12.0), together with hocomoco (version 11) human and mouse pwms, was used to detect motif enrichment in a 600 bp region centred at the peak summit., we analysed […]

PMCID: 5920086
PMID: 29700302
DOI: 10.1038/s41467-018-04111-0

[…] to further determine if bcl11b directly mediates the observed changes in the th2 program, we performed bcl11b chip-seq on cd4+ t-cells from the mlns of h. polygyrus bakeri infected mice. using the meme-chip motif analysis software, we established the conserved binding motifs for bcl11b, of which the top two are shown (fig. ). the first identified motif is a known ets-1 binding motif, […]

PMCID: 5913131
PMID: 29686312
DOI: 10.1038/s41467-018-03921-6

[…] binding site motifs. we used the top 1000 conservative narrow peaks from each b-arr, ranked by the idr peak score and included two hundred bps flanking the peak summits, for motif calling using the meme-chip suite (fig. ). analyses of the identified b-arrs motifs suggested several important conclusions. first, without any treatment, b-arrs binding motifs are very similar to each other; […]

PMCID: 5893543
PMID: 29636455
DOI: 10.1038/s41467-018-03714-x

[…] were used for further analysis, only the peaks (or part of the peaks) that were detected by macs1.4 (individual peaks p values < 1e-5) in all three samples were used for downstream analysis. meme chip ( was used to identify potential motifs within the called chip peaks. the genomic regions enrichment of annotation tool (great), […]

PMCID: 5894230
PMID: 29636001
DOI: 10.1186/s12870-018-1275-8

[…] dna after qpcr analysis)., to identify possible binding motifs of the bzip10 transcription factor, the chip peak sequences were subjected to meme (multiple em for motif elicitation)-chip []. the meme-chip program uses two ab initio motif discovery algorithms: meme [], and dreme (discriminative regular expression motif elicitation) [], which uses regular expressions to search for short […]

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MEME-ChIP institution(s)
Department of Genome Sciences, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia

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