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Protocols

iRegulon specifications

Information


Unique identifier OMICS_05264
Name iRegulon
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Stability Stable
Requirements
Cytoscape
Maintained Yes

Versioning


No version available

Documentation


Publication for iRegulon

iRegulon citations

 (40)
library_books

Peripheral tissues reprogram CD8+ T cells for pathogenicity during graft versus host disease

2018
JCI Insight
PMCID: 5922296
PMID: 29515032
DOI: 10.1172/jci.insight.97011

[…] r genes were the Notch pathway–related genes Rbpj and Furin and Notch downstream targets (Ifng, Il2ra, and Cdnk1a) (). To determine the potential regulators of M28 gene expression we used Cytoscape’s iRegulon plugin that measures enrichment for TF binding sites in the putative regulatory regions of each gene and identifies TFs predicted to bind to these motifs (e.g., EP300, HDAC2, and HES5 were pr […]

library_books

A personalized, multiomics approach identifies genes involved in cardiac hypertrophy and heart failure

2018
NPJ Syst Biol Appl
PMCID: 5825397
PMID: 29507758
DOI: 10.1038/s41540-018-0046-3

[…] co-expressed suggests that they are co-regulated. To explore this possibility, we look for enrichment in common TF binding sites in the vicinity of the 36 FC genes. To compute the enrichment, we use iRegulon, a recent algorithm integrating different TF motifs databases and using phylogenic conservation to identify overrepresented binding sites in the −20/ +20 kb regions around the Transcription S […]

library_books

Expression analysis of candidate genes for fatty acid composition in adipose tissue and identification of regulatory regions

2018
Sci Rep
PMCID: 5794915
PMID: 29391556
DOI: 10.1038/s41598-018-20473-3

[…] the TF binding sites in the promoter region of (1) the 415 genes with human orthologous ID annotated in the trans-eQTL intervals and, (2) the 43 candidate lipid-related genes was performed using the iRegulon Cytoscape plugin. The PPARG gene was the most enriched TF motif (normalized enrichment score, NES = 5.134; 167 target genes, 30 out of the 44 analyzed lipid-related candidate genes; Supplemen […]

library_books

Network analysis of SRC 1 reveals a novel transcription factor hub which regulates endocrine resistant breast cancer

2018
Oncogene
PMCID: 5895607
PMID: 29367763
DOI: 10.1038/s41388-017-0042-x

[…] C-1 regulatory network we investigated the regulons of the SRC-1 TF target genes with PWM (NFIA, SMAD2, E2F7 and ASCL1). Regulons were obtained from large scale co-expression signature datasets using iRegulon []. 79 genes were found to be regulated by two or more of the SRC-1 TFs with PWM which includes SMAD2, E2F7, ASCL1, NFIA (Fig. ).Fig. 4At the core of the TF hub two key cell cycle regulators, […]

library_books

A switch in transcription and cell fate governs the onset of an epigenetically deregulated tumor in Drosophila

2018
eLife
PMCID: 5862528
PMID: 29560857
DOI: 10.7554/eLife.32697.052

[…] ur RNA-seq dataset. We evaluated which upregulated TFs, and thus the primary response to the ph knock-out, could be contributing to the overall deregulation of gene expression observed. Employing the iRegulon tool (), predictions based on motif enrichment revealed caudal, grain and knirps (direct Ph targets in eye discs []) as TFs putatively responsible for all differentially expressed genes in ou […]

library_books

Chemokines protect vascular smooth muscle cells from cell death induced by cyclic mechanical stretch

2017
Sci Rep
PMCID: 5701048
PMID: 29170451
DOI: 10.1038/s41598-017-15867-8

[…] aLysis Toolkit, using the subnetwork enrichment analysis for “KEGG.” The predicted KEGG pathways with p < 1.00 × 10−3 are shown in Table .To identify transcription factors (TFs) for the DEGS, we used iRegulon, which exploits the fact that genes that are co-regulated by the same TFs that commonly share binding sites for the TFs and use gene sets derived from ENCODE ChIP-seq data. We used iRegulon a […]


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iRegulon institution(s)
Laboratory of Computational Biology, KU Leuven Center for Human Genetics, Leuven, Belgium; Laboratory for Molecular Cancer Biology, KU Leuven Center for Human Genetics, Leuven, Belgium

iRegulon review

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Gyan Prakash Mishra

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Desktop
iRegulon is a cytoscape App that identifies enriched motifs in cis regulatory regions for a set of genes . It allows to search within 500,10kb and 20kb to TSS. Putative transcription factor can be identified based on NES score to make gene regulatory network