motifbreakR statistics

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motifbreakR specifications

Information


Unique identifier OMICS_09712
Name motifbreakR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 1.11
Stability Stable
Requirements
IRanges, GenomicRanges, Biostrings, rtracklayer, Gviz, motifStack, MotifDb, dbsnp 20120608 142, dbsnp 20120608
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Versioning


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Documentation


Maintainer


  • person_outline Dennis J. Hazelett <>

Publication for motifbreakR

motifbreakR in publications

 (10)
PMCID: 5929547
PMID: 29715312
DOI: 10.1371/journal.pone.0196635

[…] of psoriasis through regulating gene expression via various mechanisms, for example affecting tf binding affinity. we searched for the tf motifs binding effect to each of the correlated snps using motifbreakr r package []., aberrant immune activities have been implicated widely in the pathophysiology of psoriasis. genetic variants might affect the risk of psoriasis through regulating […]

PMCID: 5891078
PMID: 29590102
DOI: 10.1371/journal.pgen.1007293

[…] as k562 experiments from the encode project were used to search for dhs and transcription factor (tf) occupancy in blood-based tissues.[, ] tf binding motif disruptions were determined using the motifbreakr r package [] and the hocomoco motif set.[] phylop calculations for 100 vertebrates were accessed using the university of california santa cruz (ucsc) genome browser []. maz, bach1, tal1, […]

PMCID: 5811556
PMID: 29440655
DOI: 10.1038/s41598-018-21024-6

[…] rs6930576, rs4607517, and rs6937795) as candidates (table ).table 2, to determine the regulatory effects of the 9 candidates on predicted transcription factor binding sites, we used the r package ‘motifbreakr’ and homer to identify the response elements broken by these snp alleles. we found that there were 58 relationships between the nine candidates and the unique predicted motifs […]

PMCID: 5801294
PMID: 29456552
DOI: 10.3389/fgene.2018.00016

[…] in tf binding between snv alleles can be predicted using position weight matrices (pwms), probabilistic representations of dna binding specificities, and motif prediction algorithms such as fimo (), motifbreakr (), beeml-pbm (), tfm-pvalue (), and motiflocator (; ) (table ). for example, motiflocator, a tool to score how mutations affect wild-type tf binding sites, led to the identification […]

PMCID: 5778810
PMID: 29379820
DOI: 10.1212/NXI.0000000000000414

[…] data prioritize these 3 snps for follow-up functional assessment. in an attempt to understand the influence of the snp position within the enhancer region in cd4+ t cells, we used the r package motifbreakr version 1.4.0 to identify putative transcription factor (tf) binding sites that were likely to be disrupted by the studied polymorphism. tf motifs were obtained from the jaspar 2014 […]


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motifbreakR institution(s)
Bioinformatics and Computational Biology Research Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Urology and Preventive Medicine, USC Norris Comprehensive Cancer Center, Los Angeles, CA, USA

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