MotifViz statistics

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Citations per year

Number of citations per year for the bioinformatics software tool MotifViz
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This map represents all the scientific publications referring to MotifViz per scientific context
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Protocols

MotifViz specifications

Information


Unique identifier OMICS_08359
Name MotifViz
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained No

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Publication for MotifViz

MotifViz citations

 (9)
call_split

The ETS factor ESE3/EHF represses IL 6 preventing STAT3 activation and expansion of the prostate cancer stem like compartment

2016
Oncotarget
PMCID: 5363547
PMID: 27732936
DOI: 10.18632/oncotarget.12525
call_split See protocol

[…] Computational search for ETS binding sites on selected gene promoters was performed using Motifviz (biowulf.bu.edu/MotifViz). Chromatin immunoprecipitation was performed with anti-ESE3 (Clone 5A5.5, Lab Vision, Fremont, CA USA); anti AcH3 (Upstate, Millipore); anti H3K9 2met (Upstate, Mill […]

library_books

ABC transporters coordinately expressed during lignification of Arabidopsis stems include a set of ABCBs associated with auxin transport

2011
J Exp Bot
PMCID: 3060696
PMID: 21239383
DOI: 10.1093/jxb/erq416

[…] Based on earlier studies of phenylpropanoid biosynthesis pathway-specific cis-elements (; ; ), 1000 bp upstream promoter regions of candidate ABC transporter genes were examined using ‘MotifViz’ (http://biowulf.bu.edu/MotifViz). Upstream promoter region sequences were obtained from the ‘The Arabidopsis Information Resource’ (TAIR) database (http://Arabidopsis.org) and analysed using […]

library_books

Identification of Genes that Elicit Disuse Muscle Atrophy via the Transcription Factors p50 and Bcl 3

2011
PLoS One
PMCID: 3020958
PMID: 21249144
DOI: 10.1371/journal.pone.0016171

[…] ndard Platinum Taq PCR reaction for 32 cycles. PCR products were separated on a 10% TBE gel (Ready Gel, BioRad) and stained by SYBR Gold.NF-κB sites for study were selected by the CLOVER algorithm of Motifviz (http://biowulf.bu.edu/MotifViz/), which uses the JASPAR database (http://jaspar.genereg.net/) for its binding matrices. We selected κB sites for ChIP that had the best score for matching the […]

library_books

DamID in C. elegans reveals longevity associated targets of DAF 16/FoxO

2010
Mol Syst Biol
PMCID: 2950082
PMID: 20706209
DOI: 10.1038/msb.2010.54

[…] To identify sequence motifs that were overrepresented in the data, we used Possum (http://biowulf.bu.edu/MotifViz/) to generate log-likelihood scores for position weight matrices (PWMs) (TRANSFAC 12.1). Within 0–2 kb upstream of genes, we defined scores above 8 as matches to a PWM. PWMs were defined as o […]

library_books

Phase Coupled Meta analysis: sensitive detection of oscillations in cell cycle gene expression, as applied to fission yeast

2009
BMC Genomics
PMCID: 2753555
PMID: 19761608
DOI: 10.1186/1471-2164-10-440

[…] her fission yeast species Schizosaccharomyces japonicus were obtained from the Schizosaccharomyces group Database at the Broad Institute of MIT and Harvard University. The motif visualization program MotifViz [] was used to detect the transcription factor binding sites with motif match p-value cutoff 0.01 and with all intergenic sequences of S. pombe and S. japonicus as background sequences for se […]

library_books

Dissecting the fission yeast regulatory network reveals phase specific control elements of its cell cycle

2009
BMC Syst Biol
PMCID: 2758837
PMID: 19758441
DOI: 10.1186/1752-0509-3-93

[…] of expression profiles from Cyclebase.org [], candidate binding sites from JASPAR [], and upstream sequences from GeneDB []. The DNA motifs were searched against JASPAR with STAMP [] and plotted with MotifViz []. The RNA motifs were identified with FIRE and RNApromo [,]. Sample skew and sample excess kurtosis of time courses were computed with the R package FinTS. The skew was computed for the fir […]


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MotifViz institution(s)
Bioinformatics Program and Biomedical Engineering Department, Boston University, Boston, MA, USA

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