IM-PET statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

IM-PET specifications

Information


Unique identifier OMICS_12565
Name IM-PET
Alternative name Integrated Methods for Predicting Enhancer Targets
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Kai Tan

Information


Unique identifier OMICS_12565
Name IM-PET
Alternative name Integrated Methods for Predicting Enhancer Targets
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Versioning


No version available

Maintainer


  • person_outline Kai Tan

Publication for Integrated Methods for Predicting Enhancer Targets

IM-PET citations

 (12)
library_books

Prediction of enhancer promoter interactions via natural language processing

2018
BMC Genomics
PMCID: 5954283
PMID: 29764360
DOI: 10.1186/s12864-018-4459-6

[…] n low-resolution experiments and high-resolution EPIs, some computational methods have been established, which mainly fall into two classes. One class is based on experimental features. For instance, IM-PET [], RIPPLE [], TargetFinder [] and EpiTensor [], aim to predict 3D genomic interactions in different cell lines by integrating numerous one-dimensional (1D) local chromatin states including gen […]

library_books

Weak sharing of genetic association signals in three lung cancer subtypes: evidence at the SNP, gene, regulation, and pathway levels

2018
Genome Med
PMCID: 5828003
PMID: 29486777
DOI: 10.1186/s13073-018-0522-9

[…] eloped a novel approach for identifying the target genes of histone-derived enhancers using a random forest classifier. The authors used this tool, Integrated Methods for Predicting Enhancer Targets (IM-PET), to define a set of enhancer target genes for 12 different cell types. We used the results for two lung cell types, IMR90 and NHLF, for our analysis. We used bedtools [] version 2.17.0 to iden […]

library_books

Identifying noncoding risk variants using disease relevant gene regulatory networks

2018
Nat Commun
PMCID: 5816022
PMID: 29453388
DOI: 10.1038/s41467-018-03133-y

[…] nomics Project, Encyclopedia of DNA Elements (ENCODE), International Human Epigenome Consortium, and the GEO database (Supplementary Table ).Target promoter(s) of an enhancer were predicted using the IM-PET algorithm. It predicts enhancer−promoter interactions by integrating four features derived from transcriptome, epigenome, and genome sequence data, including: (1) enhancer−promoter activity cor […]

library_books

Enhancing the Promise of Drug Repositioning through Genetics

2017
Front Pharmacol
PMCID: 5724196
PMID: 29270124
DOI: 10.3389/fphar.2017.00896

[…] from large-scale 3C experiments (; ). Approaches have also been developed to integrate functional genomic data to predict interactions between genes and regulatory regions (Table ; e.g., PreSTIGE and IM-PET). These approaches take advantage of the vast amount of public data provided by consortia such as ENCODE () and Roadmap Epigenomics Project (), as well as data made publicly available by resear […]

library_books

Association analysis identifies 65 new breast cancer risk loci

2017
Nature
PMCID: 5798588
PMID: 29059683
DOI: 10.1038/nature24284

[…] ions by several computational algorithms were collected. Each of these datasets assigns genes to enhancers. We used all MCF-7 and HMEC enhancer predictions (low and high stringency) made by PreSTIGE, IM-PET enhancer-gene predictions in MCF-7, HMEC and HCC1954 cell lines. Enhancer-transcription start site (E-TSS) links were identified from the FANTOM5 Consortium were identified, and enhancers detec […]

library_books

Identifying DNase I hypersensitive sites as driver distal regulatory elements in breast cancer

2017
Nat Commun
PMCID: 5585396
PMID: 28874753
DOI: 10.1038/s41467-017-00100-x

[…] Two independent experimental data sets were used to identify putative target genes of the 14,087 mutated DHSs (Fig. ): (1) 3,095,882 interactions including 3C, 4C, 5C, ChIA-PET, Hi-C, Capture-C, and IM-PET included in 4DGenome (February 1st 2015); and (2) A collection of 1,454,901 predicted distal regulatory and promoter interactions derived from the correlation of DHS peaks in promoters and dist […]

Citations

Looking to check out a full list of citations?

IM-PET institution(s)
Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, USA; Department of Internal Medicine, University of Iowa, Iowa City, IA, USA
IM-PET funding source(s)
This study was supported by National Institutes of Health Grant HG006130.

IM-PET reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review IM-PET