PWMEnrich protocols

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PWMEnrich specifications


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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  • person_outline Robert Stojnic <>

PWMEnrich in pipeline

PMCID: 5064413
PMID: 27739523
DOI: 10.1038/srep34962

[…] the ucsc database r package txdb.hsapiens.ucsc.hg19. kegg pathways enrichments were assessed by hypergeometric tests. in silico motif searches were performed with the hocomoco database using the pwmenrich package. for overlaps with chromatin states and between chip-seq datasets, the genomicranges r package was used., plasmid catalog numbers and shrna sequences are provided in . lentiviruses […]

PWMEnrich in publications

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 […]

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

[…] and for overlap with chromatin signatures, the profile for kc cells was used [] ( 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 […]

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 […]

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 […]

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 […]

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

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