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dREG specifications

Information


Unique identifier OMICS_07951
Name dREG
Alternative name discriminative Regulatory-Element detection from GRO-seq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Database management system MySQL
Computer skills Advanced
Stability Stable
Requirements
R, mysql-dev, bigWig
Maintained Yes

Download


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Versioning


No version available

Documentation


Maintainer


  • person_outline Charles Danko

Additional information


https://dreg.dnasequence.org/pages/doc

Information


Unique identifier OMICS_07951
Name dREG
Alternative name discriminative Regulatory-Element detection from GRO-seq
Interface Web user interface
Restrictions to use None
Input format BIGWIG
Computer skills Basic
Stability Stable
High performance computing Yes
Registration required Yes
Maintained Yes

Download


github.png

Documentation


Maintainer


  • person_outline Charles Danko

Additional information


https://dreg.dnasequence.org/pages/doc

Publications for discriminative Regulatory-Element detection from GRO-seq

dREG citations

 (7)
library_books

A bi stable feedback loop between GDNF, EGR1, and ERα contribute to endocrine resistant breast cancer

2018
PLoS One
PMCID: 5882141
PMID: 29614078
DOI: 10.1371/journal.pone.0194522

[…] We used dREG [] to identify the location of 39,119 transcriptional regulatory elements (TREs) that were active during at least one of the GDNF treatment time points. Comparing the location of TREs with histon […]

library_books

ER positive breast cancer cells are poised for RET mediated endocrine resistance

2018
PLoS One
PMCID: 5880349
PMID: 29608602
DOI: 10.1371/journal.pone.0194023

[…] We identified TREs using dREG []. Data collected from all four cell lines (TamR and TamS MCF-7 cells) was combined to increase statistical power for the discovery of a superset of TREs active during any of the conditions exam […]

library_books

XX Disorder of Sex Development is associated with an insertion on chromosome 9 and downregulation of RSPO1 in dogs (Canis lupus familiaris)

2017
PLoS One
PMCID: 5650465
PMID: 29053721
DOI: 10.1371/journal.pone.0186331

[…] [] to a reference genome comprised of CanFam3.1 and a single copy of the Pol I ribosomal RNA (GenBank U13369.1). Samples were visualized using custom track hubs on the WashU epigenome browser []. The dREG software program was used to identify the location of promoters and active enhancers in combined PRO-seq data [], combining male and female samples to improve statistical power for identifying tr […]

library_books

Transcriptional response to stress is pre wired by promoter and enhancer architecture

2017
Nat Commun
PMCID: 5557961
PMID: 28811569
DOI: 10.1038/s41467-017-00151-0

[…] led significant due to the activity of adjacent or partially overlapping genes (run-over transcription or internal TSS), or due to changed transcription of internal regulatory element(s), we utilized dREG. dREG is a machine-based learning method that identifies transcribed regulatory elements from the human genome using support vector regression. To call a gene significantly changed, unchanged or […]

library_books

Identifying Novel Transcriptional and Epigenetic Features of Nuclear Lamina associated Genes

2017
Sci Rep
PMCID: 5427898
PMID: 28273906
DOI: 10.1038/s41598-017-00176-x

[…] hancers in C2C12 myoblasts – 4,315 enhancers detected based on epigenomic data which will be referred to as Blum enhancers, and 5,570 putative enhancer sites identified using our GRO-seq data and the dREG method developed by Danko et al. , which will be referred to as dREG enhancers (Supplementary Table ). The two methods apparently identified two distinct sets of enhancers in that only 182 pairs […]

library_books

A generative model for the behavior of RNA polymerase

2016
Bioinformatics
PMCID: 5942361
PMID: 27663494
DOI: 10.1093/bioinformatics/btw599

[…] 3K4me1/3) may be predicted from bidirectional transcription alone. With an HCT116 GRO-seq dataset (), we benchmarked our method against the current state-of-the-art bidirectional detection algorithm, dREG (). The BIC penalty α (Tfit) and support vector regression score (dREG) was varied. True positives were considered as an overlap with chromatin mark peaks (HCT116 (), MACS broad peak settings) an […]

Citations

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dREG institution(s)
Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA; Graduate field of Computational Biology, Cornell University, Ithaca, NY, USA; Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA

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