TIP statistics

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Citations per year

Number of citations per year for the bioinformatics software tool TIP
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Tool usage distribution map

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

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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

Versioning


No version available

Maintainer


  • person_outline Mark Gerstein

Publication for Target Identification from Profiles

TIP citations

 (3)
library_books

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

2017
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 […]

library_books

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

2015
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 […]

library_books

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

2013
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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avilella

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Desktop
Single R script. No documentation.