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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 citations


NOTCH mediated non cell autonomous regulation of chromatin structure during senescence

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 […]


Bcl11b is essential for licensing Th2 differentiation during helminth infection and allergic asthma

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, […]


A B ARR mediated cytokinin transcriptional network directs hormone cross regulation and shoot development

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; […]


Genome wide (ChIP seq) identification of target genes regulated by BdbZIP10 during paraquat induced oxidative stress

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 […]


NKX2 5 regulates human cardiomyogenesis via a HEY2 dependent transcriptional network

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), […]


Tuning Hsf1 levels drives distinct fungal morphogenetic programs with depletion impairing Hsp90 function and overexpression expanding the target space

PMCID: 5873724
PMID: 29590106
DOI: 10.1371/journal.pgen.1007270

[…] parameters. hsf1 binding peaks were identified by model-based analysis of chip-seq (macs)[] using standard parameters with -log10(q-value) cutoff of 50. de novo motif discovery was performed using meme-chip on 200 bp sequences spanning hsf1 summits reported by macs (i.e. 100 bp on each side of summits)[]. hsf1 target genes were identified by mapping genes with atg closest to hsf1 binding sites […]

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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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