iRegulon 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

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Documentation


Publication for iRegulon

iRegulon IN pipelines

 (4)
2017
PMCID: 5548054
PMID: 28713939
DOI: 10.3892/mmr.2017.6933

[…] using the toppgene database. the reactomefiviz application was used to construct functional interaction (fi) networks, and the genes in each module were subjected to pathway enrichment analysis. the iregulon plugin was used to identify transcription factors predicted to regulate the degs in the fi network, and the gene-transcription factor pairs were then visualized using cytoscape software. […]

2017
PMCID: 5772172
PMID: 29262348
DOI: 10.1016/j.immuni.2017.11.024

[…] (nodes) are connected, if the correlation value calculated between their expression profiles was at least 0.9., to predict master regulators for each of the four cell types, the cytoscape app iregulon v1.3 was applied on those genes of the cell type specific clusters identified within the co-expression network, which were upregulated in the corresponding cell type compared to the overall […]

2016
PMCID: 5352132
PMID: 27888795
DOI: 10.18632/oncotarget.13440

[…] line for a gene with a slope > 0.4 or < −0.4, which indicated gene up- or downregulated, respectively. to gain insight into transcriptional programs downstream of tacr1 receptor signalling, iregulon analysis, a cytoscape plugin to identify regulons in a set of co-regulated genes using motif discovery, was performed on up- and downregulated genes [31]. a regulon consists […]

2015
PMCID: 4448502
PMID: 26023727
DOI: 10.1038/srep10624

[…] 67 binding domain motifs, with 47 unique transcription factors, were found. of these, srebp1 and srebp2 were pulled out at the top of the list. this was completed using a plugin for cytoscape called iregulon25 and the output is included in the supplemental as table st4. we combined genes regulated by srebp1/srebp2 and egr1/egr2 as well as fold change expression values for all three treatment […]

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