coMOTIF statistics

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Number of citations per year for the bioinformatics software tool coMOTIF
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coMOTIF specifications

Information


Unique identifier OMICS_17695
Name coMOTIF
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0
Stability Stable
Source code URL https://www.niehs.nih.gov/research/resources/assets/docs/comotif_v10targz.gz
Maintained Yes

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Publication for coMOTIF

coMOTIF citations

 (4)
library_books

Modular discovery of monomeric and dimeric transcription factor binding motifs for large data sets

2018
Nucleic Acids Res
PMCID: 5934673
PMID: 29385521
DOI: 10.1093/nar/gky027

[…] ize the techniques of MEME (,) to multi-profile dimeric case. As compared to MEME, an important feature of MODER is that it learns all submodels simultaneously, using all training data symmetrically. coMOTIF () is another simultaneous multi-profile motif finder based EM algorithm. It does not, however, keep track of the distances between binding sites and does not allow overlaps of binding sites, […]

library_books

Evaluating the impact of single nucleotide variants on transcription factor binding

2016
Nucleic Acids Res
PMCID: 5137422
PMID: 27492288
DOI: 10.1093/nar/gkw691

[…] nding model (). The comotifs lay in three categories (Supplementary Table S3): (i) seven cases in which the TFs associated to the comotifs were known to interact with the ChIP'ed TF, for instance the comotif of P300 was CEBPB (P300-CEBPB); (ii) one case (RUNX3-RUNX1) in which the TF of comotif belonged to the same TF family as the ChIP'ed TF; and (iii) seven cases of novel relationships, from our […]

library_books

Translational Bioinformatics for Diagnostic and Prognostic Prediction of Prostate Cancer in the Next Generation Sequencing Era

2013
Biomed Res Int
PMCID: 3727129
PMID: 23957008
DOI: 10.1155/2013/901578

[…] is of AR and ERG binding sites. They revealed that ERG promotes prostate cancer progression by working together with transcriptional corepressors including HDACs and EZH2. Zhang et al. [] developed a comotif scanning program called CENTDIST and applied it on an AR ChIP-Seq dataset from a prostate cancer cell line. They correctly predicted all known co-TFs of AR as well as discovered AP4 as a novel […]

library_books

Whole Genome Cartography of Estrogen Receptor α Binding Sites

2007
PLoS Genet
PMCID: 1885282
PMID: 17542648
DOI: 10.1371/journal.pgen.0030087

[…] overlap specifically at the ERE site itself, the most striking being SF1 and PAX3. It did not escape our attention that the observed overlap could be arising from the inherent similarity of the other comotif with ERE or half-site ERE. However, if we use a validated cofactor AP-1 as a model, upon alignment of all the sequences of the AP-1 binding sites and their associated ERE (see ), we discovered […]


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coMOTIF institution(s)
Biostatistics Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
coMOTIF funding source(s)
This work was supported by Intramural Research Program of the National Institutes of Health; National Institute of Environmental Health Sciences (ES101765-05).

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