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PWMEnrich specifications

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Unique identifier OMICS_23142
Name PWMEnrich
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 4.12.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Robert Stojnic <>

PWMEnrich citations

 (14)
library_books

Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes

2018
PMCID: 5958058
PMID: 29773832
DOI: 10.1038/s41467-018-04383-6

[…] enrichment analysis using the chea database (fisher exact test on the basal-classical component associated genes) or by motif enrichment on the basal-classical component associated regions using pwmenrich r package. tfs, for which expression was negatively or positively correlated to the basal-classical component, were regarded as classical or basal tfs, respectively. cytoscape was used […]

library_books

Role of co repressor genomic landscapes in shaping the Notch response

2017
PMCID: 5714389
PMID: 29155828
DOI: 10.1371/journal.pgen.1007096

[…] and for overlap with chromatin signatures, the profile for kc cells was used [] (https://github.com/rstojnic/notch-chromatin). motif enrichment analysis was performed using the bioconductor package pwmenrich [], which assesses the enrichment of each motif from a library of 650 experimentally derived dna motifs for drosophila transcription factors. accessible chromatin in bg3 and kc167 cells […]

library_books

Transcriptome profiling revealed novel transcriptional regulators in maize responses to Ostrinia furnacalis and jasmonic acid

2017
PMCID: 5433750
PMID: 28520800
DOI: 10.1371/journal.pone.0177739

[…] collection of plant position weight matrices (pwms) [] and also pwms deposited in the jaspar database were used. promoters were scanned for significantly enriched cis-elements using the pwmenrich package in the bioconductor project., maize protoplast preparation and peg-mediated transfection was performed as previously described []. a modified version of pcambia3300, referred […]

library_books

Widespread promoter methylation of synaptic plasticity genes in long term potentiation in the adult brain in vivo

2017
PMCID: 5364592
PMID: 28335720
DOI: 10.1186/s12864-017-3621-x

[…] imported from maag et al. 2015, and plotted against logfc methylation between each time point and control., investigation for motifs present in correlated vs. non-correlated genes was done using pwmenrich []. for the promoter region comparison region 1 kb upstream from the promoter were investigated for motifs. a background object was created using makepwmlognbackground for all mus musculus […]

library_books

Transcription factor TFCP2L1 patterns cells in the mouse kidney collecting ducts

2017
PMCID: 5484618
PMID: 28577314
DOI: 10.7554/eLife.24265.044

[…] to patterning collecting duct cell types., ‘notch-on’ signaling may be relevant to cell fate choices because while hes1 targets are not known in detail, tf binding site overrepresentation analysis (pwmenrich; ) of tfcp2l1 bound peaks demonstrated neighboring tfcp2l1 and hes1 binding sites, as well as combinatorial binding of tfcp2l1-foxi1-hes1 () raising the possibility that hes1 signaling […]

library_books

Transcription factor dependent enhancer transcription defines a gene regulatory network for cardiac rhythm

2017
PMCID: 5745077
PMID: 29280435
DOI: 10.7554/eLife.31683.021

[…] e2f, that provide non-tissue-specific transcriptional functions (). by contrast, tbx5-activated enhancers showed significant enrichment for the t-box motif itself (enrichment score = 6.7, p=0.03, pwmenrich []). furthermore, tbx5 occupancy by chip-seq in atrial hl-1 cells () was highly enriched at open atrial locations that contained tbx5-dependent ncrnas (72 of the 152 locations, or = 18, […]


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PWMEnrich institution(s)
Cambridge Systems Biology Institute, University of Cambridge, UK

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