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WebMOTIFS specifications

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Unique identifier OMICS_06275
Name WebMOTIFS
Interface Web user interface
Restrictions to use Academic or non-commercial use
Computer skills Basic
Stability No
Maintained No

Publication for WebMOTIFS

WebMOTIFS citations

 (5)
library_books

Nuc‐ErbB3 regulates H3K27me3 levels and HMT activity to establish epigenetic repression during peripheral myelination

2016
PMCID: 5021170
PMID: 27017927
DOI: 10.1002/glia.22977

[…] regions masked using the built‐in repeat masking algorithm in the ucsc genome browser and tandem repeat finder (benson, ). de novo motif discovery was performed using the command‐line version of webmotifs (romer et al., ). the set of 75 peak sequences was used in three different motif discovery programs: alignace (hughes et al., ), weeder (pavesi et al., ) and mdscan (liu et al., ). […]

library_books

Genome Wide Analysis of Transcriptional Reprogramming in Mouse Models of Acute Myeloid Leukaemia

2011
PMCID: 3030562
PMID: 21297973
DOI: 10.1371/journal.pone.0016330

[…] expressed genes using two of the most widely used tools for this type of in silico analysis, opossum only identified the binding site for one of the 19 factors shown in (i.e. cebpa) and webmotifs failed to identify any significant motifs at all (see figure s11 in ). by contrast, our direct measurements of differential levels of histone acetylation allowed us to select […]

library_books

Combination of genomic approaches with functional genetic experiments reveals two modes of repression of yeast middle phase meiosis genes

2010
PMCID: 3091674
PMID: 20716365
DOI: 10.1186/1471-2164-11-478

[…] and is also enriched for the cell division go category (p = 0.0018), a mitotic related category, intimately associated with meiotic divisions as well. second, using de novo motif search algorithms (webmotifs; http://fraenkel.mit.edu/webmotifs/ and []), we found that the promoters of these genes are highly enriched for the presence of the middle sporulation element (mse) (specificity score […]

library_books

Reconstruction of Gene Regulatory Modules in Cancer Cell Cycle by Multi Source Data Integration

2010
PMCID: 2858157
PMID: 20422009
DOI: 10.1371/journal.pone.0010268

[…] database (http://www.sabiosciences.com/chipqpcrsearch.php?app=tfbs)., finally, we determined how many genes in the gene clusters have e2f binding sites. we applied the motif discovery tool, webmotifs to find shared motifs in the gene clusters predicted to the e2f targets using binding site enrichment analysis (bsea). the results revealed that a motif called e2f_tdp, gcgssaaa, […]

library_books

Network motif based identification of transcription factor target gene relationships by integrating multi source biological data

2008
PMCID: 2386822
PMID: 18426580
DOI: 10.1186/1471-2105-9-203

[…] regulates donor preference during switching. to further investigate the possibilities that the predicted downstream gene clusters are truly regulated by fkh1, we applied the motif discovery tool, webmotifs [] to find shared motifs in these gene clusters. the results revealed that a motif called fork_head, gtaaacaa, is identified as the most significant motif among these gene clusters []. […]


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WebMOTIFS institution(s)
Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA

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