DiRE protocols

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DiRE specifications

Information


Unique identifier OMICS_21237
Name DiRE
Alternative names Distance Regulatory Elements of co-regulated genes, CREME
Interface Web user interface
Restrictions to use None
Input data A gene name.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Ivan Ovcharenko <>

Publication for Distance Regulatory Elements of co-regulated genes

DiRE in pipelines

 (4)
2017
PMCID: 5335607
PMID: 28256583
DOI: 10.1038/srep43765

[…] were constructed using the java applet venny, http://bioinfogp.cnb.csic.es/tools/venny/index.html., prediction of tfbs was performed using either distant regulatory elements of co-regulated genes (dire) or gene set enrichment analysis (gsea). sensitivity of dire in predicting tfbs enrichment was validated by analysis of gene sets corresponding to (a) vp16 constitutively active creb (526 […]

2011
PMCID: 3248441
PMID: 22242143
DOI: 10.1371/journal.pone.0029758

[…] expression patterns compared to twist1 (). thus expression of the twist1 downstream candidate genes sema3c, tubb3, rab39b, gadd45a, and serpinb9b is similar totwist1 during heart valve development., dire, trafac, rvista2.0, and opossum analyses were employed to identify ecrs containing e-box consensus sequences associated with twist1 candidate target genes identified through microarray gene […]

2011
PMCID: 3248441
PMID: 22242143
DOI: 10.1371/journal.pone.0029758

[…] a single e-box consensus sequence. conversely, cdh11-intron1 contains 2 e-box consensus sequences, however, twist1 binding and gene induction was detected only for e-box1. rvista2.0, opossum, dire, and trafac analysis for transcription factor binding sequences revealed that each identified enhancer has additional conserved transcription factor binding consensus sequences –. enhancer […]

2010
PMCID: 3091648
PMID: 20659319
DOI: 10.1186/1471-2164-11-451

[…] immunoprecipitation; ciz: cas-associated zinc finger protein; clover: cis-element over-representation; cmv: cytomegalovirus; david: database for annotation, visualization and integrated discovery; dire: distant regulatory elements of co-regulated genes; dlk1: delta-like 1 homolog; ecr: evolutionarily conserved regions; egf: epidermal growth factor; egr: early growth response; elf5: […]


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DiRE in publications

 (19)
PMCID: 5335607
PMID: 28256583
DOI: 10.1038/srep43765

[…] regulated by specific action potential firing patterns, we analyzed transcriptome data by two techniques: an enhancer identification method through distant regulatory elements of co-regulated genes (dire) and by gene set enrichment analysis (gsea). the sensitivity of dire was validated by analyzing transcriptome data where either creb-regulated genes (526 genes), nf-κb regulated genes (403 […]

PMCID: 5303304
PMID: 28187790
DOI: 10.1186/s13073-017-0407-3

[…] higher mycn expression levels (additional file : figure s5a). similarly, a proportion of the genes bound by mycn have known smad regulatory elements (additional file : figure s5b), as revealed by dire analysis []. smads are the direct and prime transcriptional effectors of tgf-β signalling [, ]. in addition, genes bound by mycn in kcnr cells were enriched for the tgf-β signalling pathway, […]

PMCID: 5115891
PMID: 27713115
DOI: 10.18632/aging.101049

[…] the biomart package (http://www.biomart.org/) biomart ver. 0.8 rc3 (version 0.8 of release candidate 3)., to predict common regulatory elements (res) for our input genes, we used a web server called dire (distant regulatory elements of coexpressed genes, http://dire.dcode.org/), which is based on the enhancer identification (ei) method for predicting distant regulatory elements in higher […]

PMCID: 5104194
PMID: 27895744
DOI: 10.3892/ol.2016.5180

[…] cells. a gene count between 15 and 500 and p<0.01 were set as the criteria to filter the pre-defined gene sets. in addition, the distant regulatory elements of co-regulated genes tool (http://dire.dcode.org), which enables the prediction of distant regulatory elements in higher eukaryotic genomes (), was applied to screen for transcription factors associated with the degs in the enriched […]

PMCID: 5312386
PMID: 27531891
DOI: 10.18632/oncotarget.11203

[…] analysis. all sequencing samples were performed in biological duplicate and sequenced on an illumina gaiix or hiseq 2500. mycn's genomic targets were analysed for known regulatory elements using the dire [] tool (http://dire.dcode.org)., ingenuity pathway analysis (ipa) software was also used for the itr, pathway and gene ontology (go) analysis for all omics samples. string (www.string-db.org) […]


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DiRE institution(s)
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
DiRE funding source(s)
Supported by the Intramural Research Program of the National Institutes of Health, National Library of Medicine.

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