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 in publications

 (4)
PMCID: 5934673
PMID: 29385521
DOI: 10.1093/nar/gky027

[…] 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, […]

PMCID: 5137422
PMID: 27492288
DOI: 10.1093/nar/gkw691

[…] 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, […]

PMCID: 3727129
PMID: 23957008
DOI: 10.1155/2013/901578

[…] 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 […]

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

[…] 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 ), […]


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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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