BioNet statistics

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Citations per year

Number of citations per year for the bioinformatics software tool BioNet

Tool usage distribution map

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

This word cloud represents BioNet usage per disease context

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BioNet specifications


Unique identifier OMICS_06989
Name BioNet
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained No


No version available

Publication for BioNet

BioNet citations


Identification of key genes associated with bladder cancer using gene expression profiles

PMCID: 5766060
PMID: 29375713
DOI: 10.3892/ol.2017.7310

[…] of the PPI network was performed using Cytoscape software ( (). The HUB nodes with the top 5 degrees in the PPI network were also obtained.The PPI sub-network of DEGs was identified by BioNet (), and a false discovery rate of <0.01 was selected as the threshold criterion. The pathway enrichment analysis of genes in the core PPI sub-network was performed using the KEGG database, and […]


Molecular mechanisms of breast cancer metastasis by gene expression profile analysis

PMCID: 5647040
PMID: 28791367
DOI: 10.3892/mmr.2017.7157

[…] To further explore the key nodes for breast cancer metastasis, a subnetwork was established comprising 44 nodes using the BioNet tool, among which spleen tyrosine kinase (SYK) was predominant with the highest degree (degree=10; ). KEGG pathway enrichment analysis indicated that proteins in the subnetwork, in which SYK wa […]


Incorporating interaction networks into the determination of functionally related hit genes in genomic experiments with Markov random fields

PMCID: 5870666
PMID: 28881978
DOI: 10.1093/bioinformatics/btx244

[…] the results presented in the paper, which is freely available for modification.We have shown that our MRF method gave the best results in a simulation experiment originally used to evaluate Knode and BioNet. We have additionally shown that we were able to find greater pathway enrichment as well as further determine hit genes in a lymphoma study concerning survival analysis and gene expression, whe […]


Bioinformatics analysis of transcription profiling of solid pseudopapillary neoplasm of the pancreas

PMCID: 5562055
PMID: 28627654
DOI: 10.3892/mmr.2017.6800

[…] eneral Medical Sciences, Bethesda, MD, USA).The identification of significantly differentially expressed sub-networks within a large network is the primary task when a PPI network is constructed. The BioNet package (version 2.1) () was employed for sub-network analysis, and FDR<0.0001 was set as the cut-off criterion. KEGG enrichment analysis was also performed at the sub-network level. […]


Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence

BMC Genomics
PMCID: 5383966
PMID: 28388876
DOI: 10.1186/s12864-017-3616-7

[…] en derived from the limma analyses. For the integrated network analysis node (gene) scores have been computed based on these p-values as detailed in [] using the routines implemented in the R-package BioNet []. […]


Prior knowledge guided active modules identification: an integrated multi objective approach

BMC Syst Biol
PMCID: 5374590
PMID: 28361699
DOI: 10.1186/s12918-017-0388-2

[…] To estimate distribution for p-values, the parameters of BUM model a and λ are estimated by R package BioNet []. Figure shows the fitted model. As the majority of genes in yeast network have a very significant p-value, threshold τ is calculated at an extremely stringent FDR level as an attempt to con […]

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BioNet institution(s)
Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany

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