CyTargetLinker protocols

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CyTargetLinker specifications

Information


Unique identifier OMICS_27549
Name CyTargetLinker
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 3.0.1
Stability Stable
Requirements
Cytoscape
Maintained Yes

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Maintainer


  • person_outline Martina Kutmon <>

Additional information


http://apps.cytoscape.org/apps/cytargetlinker

Publication for CyTargetLinker

CyTargetLinker in pipelines

 (7)
2017
PMCID: 5370130
PMID: 28350871
DOI: 10.1371/journal.pone.0174514

[…] was obtained from the mirbase website (http://www.mirbase.org/) []. sequencing data have been deposited in the geo database (gse93020)., gene target identification for mirnas was performed using the cytargetlinker application in cytoscape. firstly, candidate mirnas identified from the sequencing data was imported into cytoscape. a total of 3 mirna gene target databases (microcosm, mirtarbase […]

2017
PMCID: 5531511
PMID: 28749975
DOI: 10.1371/journal.pone.0180329

[…] at the ncbi gene expression omnibus (geo, http://www.ncbi.nih.gov/geo/) gse74770., a regulatory network between mirna and genes was created with usage of cytoscape (http://www.cytoscape.org/) [] and cytargetlinker (http://projects.bigcat.unimaas.nl/cytargetlinker/) [] with regulatory interaction in network analysis (regin) mirtarbase release 6.1 […]

2016
PMCID: 4725832
PMID: 26757825
DOI: 10.1038/srep19416

[…] of lncrna networks was performed by retrieving clip-seq data based prediction of lncrna-mirna interactions using starbase v2.0. networks were extended by target analysis of mirna lists using the cytargetlinker together with cytoscape and cluego analysis annotated functionally grouped gene ontologies and pathways. following settings were considered for cluego analysis: significant kegg […]

2016
PMCID: 4725832
PMID: 26757825
DOI: 10.1038/srep19416

[…] was subjected to target analysis and a network of mrnas was generated that were inferred to cross talk to the lncrna via mutual mre. for this purpose, we employed cytoscape together with its app cytargetlinker and predicted mirna-mrna networks by considering regulatory interaction networks of target scan. the resulting target networks (mrna sharing mres with lncrna) of an identified lncrna […]

2016
PMCID: 5456327
PMID: 28933415
DOI: 10.3390/diseases4040035

[…] genes (from an initial gene number of 14) with asthma, obesity, alzheimer's disease and malignant neoplasm of the breast ()., network analysis with regulatory interactions was performed using the cytargetlinker app for cytoscape in order to find mirna-target, transcription factor-target or drug-target interactions for both dataset groups (naïve and ert patients) (). for this, regulatory data […]


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CyTargetLinker in publications

 (13)
PMCID: 5840996
PMID: 29451210
DOI: 10.4103/1673-5374.224374

[…] target mrnas in the nac following intravenous self-administration of morphine. we utilized several bioinformatics tools, including kyoto encyclopedia of genes and genomes (kegg) pathway mapping and cytargetlinker. we found that 62 mirnas were altered and exhibited differential expression patterns. the putative targets were related to diverse regulatory functions, such as neurogenesis, […]

PMCID: 5615414
PMID: 29018475
DOI: 10.3389/fgene.2017.00116

[…] of text mined extracted pair associations (mirna-lipid disease) were estimated by one-sided fisher's exact test. the top 20 significant mirna-disease associations were visualized on cytoscape. the cytargetlinker plug-in tool on cytoscape was used to extend the network and predicts new mirna target genes. the biological networks gene ontology (bingo) plug-in tool on cytoscape was used […]

PMCID: 5531511
PMID: 28749975
DOI: 10.1371/journal.pone.0180329

[…] at the ncbi gene expression omnibus (geo, http://www.ncbi.nih.gov/geo/) gse74770., a regulatory network between mirna and genes was created with usage of cytoscape (http://www.cytoscape.org/) [] and cytargetlinker (http://projects.bigcat.unimaas.nl/cytargetlinker/) [] with regulatory interaction in network analysis (regin) mirtarbase release 6.1 […]

PMCID: 5491496
PMID: 28663595
DOI: 10.1038/s41598-017-04300-9

[…] to stress and psychiatric disorders. further analysis on predicted and validated target genes of differentially expressed mirnas were carried out using mirpath (version 3) from diana tools and cytargetlinker plugin from cytoscape software (version 3.0). the purpose of these advanced analyses was to find out affected pathways in relation to pathophysiological state and linking with the gene […]

PMCID: 5499856
PMID: 28721073
DOI: 10.2147/OTT.S135764

[…] studies also validated that the six mirnas can differentiate prostate cancer patients from healthy people with 89% accuracy. based on the six mirnas, we constructed the regulation network using cytargetlinker plugin in cytoscape. in brief, target genes for the six mirnas were predicted using microcosm, mirtarbase and targetscan databases. then, intersection between the common degs […]


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CyTargetLinker institution(s)
Department of Bioinformatics - BiGCaT, NUTRIM School for Nutrition, Toxicology and Metabolism, University of Maastricht, Maastricht, The Netherlands; Netherlands Consortium for Systems Biology (NCSB), Amsterdam, The Netherlands; TNO, Research Group Microbiology and Systems Biology, Zeist, The Netherlands

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