NetworkAnalyzer statistics

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Citations per year

Number of citations per year for the bioinformatics software tool NetworkAnalyzer
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Tool usage distribution map

This map represents all the scientific publications referring to NetworkAnalyzer per scientific context
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Associated diseases

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Protocols

NetworkAnalyzer specifications

Information


Unique identifier OMICS_12238
Name NetworkAnalyzer
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


Maintainer


  • person_outline Mario Albrecht

Publications for NetworkAnalyzer

NetworkAnalyzer citations

 (200)
library_books

Identification of potential crucial genes and construction of microRNA mRNA negative regulatory networks in osteosarcoma

2018
Hereditas
PMCID: 5941338
PMID: 29760609
DOI: 10.1186/s41065-018-0061-9

[…] PPI network of the DEGs []. The interaction score of not < 0.7 (high confidence score) was considered significant and the PPI was visualized.The relationships among the DEGs were analyzed by plug-in NetworkAnalyzer of Cytoscape software for the characteristics of small-world network through calculating the network properties such as distribution of network node degree, distribution of the shortes […]

library_books

Integrative Transcriptomic Analysis Uncovers Novel Gene Modules That Underlie the Sulfate Response in Arabidopsis thaliana

2018
Front Plant Sci
PMCID: 5902692
PMID: 29692794
DOI: 10.3389/fpls.2018.00470

[…] e best fit of the scale-free topology, as described previously (). The gene co-expression network was visualized using Cytoscape v3.4 (), and the network topology parameters were calculated using the NetworkAnalyzer plugin (). Co-expression modules were identified using Dynamic Tree Cut software (). […]

library_books

Microbiome of Total Versus Live Bacteria in the Gut of Rex Rabbits

2018
Front Microbiol
PMCID: 5902543
PMID: 29692775
DOI: 10.3389/fmicb.2018.00733

[…] One thousand permutations and bootstrap scores were generated. Edges with merged P-values < 0.01 were kept (Benjamini–Hochberg correction). Networks were visualized via Cytoscape 3.4 (), applying the Networkanalyzer plugin analysis for network characteristics.The Mann–Whitney U-test was used to examine the statistical significance of the alpha and beta diversities and the degree of networks via SP […]

call_split

A systems pharmacology oriented discovery of a new therapeutic use of the TCM formula Liuweiwuling for liver failure

2018
Sci Rep
PMCID: 5884779
PMID: 29618826
DOI: 10.1038/s41598-018-21515-6
call_split See protocol

[…] e specified network of the selected disease was rebuild and Cytoscape V3.2 was applied to visualize and analyse the network. The topological features of each node in the network were calculated using NetworkAnalyzer in the Cytoscape software and the most possible diseases targets that Liuweiwuling might act on were screened with three topologic parameters: “Degree”, “Betweenness Centrality” and “C […]

library_books

From SNPs to pathways: Biological interpretation of type 2 diabetes (T2DM) genome wide association study (GWAS) results

2018
PLoS One
PMCID: 5884486
PMID: 29617380
DOI: 10.1371/journal.pone.0193515

[…] network nodes, we conducted both a network topology investigation and an integration of information from other data sources. In particular, we studied the node degree distribution using the Cytoscape NetworkAnalyzer module [] and we integrated additional information from other databases and sources, such as: GeneCards (gene description), Ensembl (gene and variants description), DisGeNET (evidences […]

library_books

Strongyle Infection and Gut Microbiota: Profiling of Resistant and Susceptible Horses Over a Grazing Season

2018
Front Physiol
PMCID: 5871743
PMID: 29618989
DOI: 10.3389/fphys.2018.00272

[…] r correlation, we constructed co-occurrence networks. The cutoff of p-values was 0.05. The cutoff of correlation coefficients was determined as r ≥ |0.35|. Network properties were calculated with the NetworkAnalyzer plugin in Cytoscape. We used the “iGraph” package in R to visualize the network. Strong and significant correlation between nodes (r ≥ |0.60|) were represented with larger edge width i […]


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NetworkAnalyzer institution(s)
Max Planck Institute for Informatics, Saarbrücken, Germany; Center for Biomedicine, EURAC research, Bolzano, Italy; Institute of Biometrics and Medical Informatics, University Medicine Greifswald, Greifswald, Germany
NetworkAnalyzer funding source(s)
Supported by the BMBF through the German National Genome Research Network (NGFN) and the Greifswald Approach to Individualized Medicine (GANI_MED), in the context of the DFG-funded Cluster of Excellence for Multimodal Computing and Interaction.

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