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Citations per year

Number of citations per year for the bioinformatics software tool DiRE

Tool usage distribution map

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


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


  • person_outline Ivan Ovcharenko

Publication for Distance Regulatory Elements of co-regulated genes

DiRE citations


Gene networks activated by specific patterns of action potentials in dorsal root ganglia neurons

Sci Rep
PMCID: 5335607
PMID: 28256583
DOI: 10.1038/srep43765

[…] rams 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 transcr […]


Retinoic acid and TGF β signalling cooperate to overcome MYCN induced retinoid resistance

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

[…] ith 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, as r […]


Investigating regulatory signatures of human autophagy related gene 5 (ATG5) through functional in silico analysis

PMCID: 5006144
PMID: 27617225
DOI: 10.1016/j.mgene.2016.07.012

[…] The web based server DiRE was used to identify the distant regulatory elements (REs) in the ATG5 gene. The program was run with the default value for random set of genes as 5000. Through this analysis, two potential regul […]


Limited but durable changes to cellular gene expression in a model of latent adenovirus infection are reflected in childhood leukemic cell lines

PMCID: 4946252
PMID: 27085068
DOI: 10.1016/j.virol.2016.03.015

[…] ological clusters.To see if the coordinately regulated genes share common transcriptional regulators, genes identified in patterns 1 through 4 were analyzed with the Distant Regulatory Elements () or DiRE tool (http://dire.dcode.org/). The number of genes in patterns 5 and 6 were below the recommended number for analysis. DiRE generates a weighted list of known regulatory elements based on their a […]


In vitro reversion of activated primary human hepatic stellate cells

PMCID: 4527231
PMID: 26251672
DOI: 10.1186/s13069-015-0031-z

[…] tein 1 (SP1) were predicted to be the transcription factors with the highest importance and occurrence score, respectively, for the binding of common regulatory elements for this set of genes (http://dire.dcode.org/). SRF is mainly involved in cell differentiation by regulating genes that control cell growth, cytoskeletal organization, contractility, and motility []. In rodent HSCs, Srf expression […]


Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations

Nat Commun
PMCID: 4166678
PMID: 25182477
DOI: 10.1038/ncomms5767

[…] th a minimal twofold change in expression were subjected to functional enrichment analysis using DAVID and IPA (Ingenuity Systems, www.ingenuity.com), transcription factor regulation prediction using DiRE and manual inspection. Those lists are available as . For integration in the IGV genome browser, we chose to display all genes found to be differentially expressed (BH-adjusted P value<0.01) in t […]

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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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