TIP statistics

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Citations per year

Number of citations per year for the bioinformatics software tool TIP

Tool usage distribution map

This map represents all the scientific publications referring to TIP per scientific context
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TIP specifications


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


No version available


  • person_outline Mark Gerstein

Publication for Target Identification from Profiles

TIP citations


Inferring condition specific targets of human TF TF complexes using ChIP seq data

BMC Genomics
PMCID: 5223348
PMID: 28068916
DOI: 10.1186/s12864-016-3450-3

[…] red 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 are sugge […]


Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes

PMCID: 4666684
PMID: 26446758
DOI: 10.3109/10409238.2015.1087961

[…] ne expression; such methods include partial least squares (PLS) regression (Boulesteix & Strimmer, ), a genetic regulatory modules (GRAM) algorithm (Bar-Joseph et al., ), a probabilistic model termed target identification from profiles (TIP) (Cheng et al., ), a support vector machine (SVMs) (Qian et al., ), a linear activation model based (Honkela et al., ), and an unsupervised machine learning wi […]


Transcription Factor Binding Profiles Reveal Cyclic Expression of Human Protein coding Genes and Non coding RNAs

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

[…] h 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 in ma […]

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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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Single R script. No documentation.