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BioNet specifications

Information


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

Versioning


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Publication for BioNet

BioNet citations

 (41)
library_books

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

2017
PMCID: 5766060
PMID: 29375713
DOI: 10.3892/ol.2017.7310

[…] of the PPI network was performed using Cytoscape software (cytoscape.org) (). 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 […]

library_books

Molecular mechanisms of breast cancer metastasis by gene expression profile analysis

2017
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 […]

library_books

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

2017
Bioinformatics
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 […]

library_books

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

2017
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. […]

library_books

Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence

2017
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 []. […]

library_books

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

2017
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 […]

Citations

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

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