TIP specifications

Information


Unique identifier OMICS_13464
Name TIP
Alternative name Target Identification from Profiles
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
Stability Stable
Source code URL http://archive.gersteinlab.org/proj/tftarget/data/functions.R
Maintained Yes

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Maintainer


  • person_outline Mark Gerstein <>

Publication for Target Identification from Profiles

TIP in publications

 (2)
PMCID: 5223348
PMID: 28068916
DOI: 10.1186/s12864-016-3450-3

[…] with those by spamo. the peak enrichment for cst was approximately 32 (at the 40% confidence decile), whereas that for spamo was approximately 18 (at the 60% decile). these results indicated that target identification from profiles (tip) method [] together with spamo, equivalent to cst, significantly improved the prediction of tf complexes over the use of spamo alone. similar results […]

PMCID: 3708869
PMID: 23874175
DOI: 10.1371/journal.pcbi.1003132

[…] provided high-resolution binding events of more than 120 human tfs in multiple cell lines. the binding strength of a tf to the promoters of genes was calculated by a probabilistic model called tip (target identification from profiles) we proposed previously . this model provides a significantly more accurate measure of tf binding affinity to particular genes than the peak-based method used […]


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TIP institution(s)
Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Computer Science, Yale University, New Haven, CT, USA
TIP funding source(s)
This work was supported by National Institutes of Health.

TIP review

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Desktop
Single R script. No documentation.