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FGNet specifications


Unique identifier OMICS_07433
Name FGNet
Alternative name Functional Gene Networks
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 3.14.0
Stability Stable
AnnotationDbi, KEGG.db, RColorBrewer, BiocGenerics, R(>=2.15), RUnit, rmarkdown, knitr, plotrix, reshape2, GO.db, reactome.db, RCurl, hwriter, org.Sc.sgd.db, topGO, R.utils, igraph(>=0.6), XML, png, gage, RGtk2, RDAVIDWebService, KEGGprofile
Maintained Yes


No version available



  • person_outline Sara Aibar

Publication for Functional Gene Networks

FGNet citations


Using Human iPSC Derived Neurons to Uncover Activity Dependent Non Coding RNAs

PMCID: 5748719
PMID: 29261115
DOI: 10.3390/genes8120401
call_split See protocol

[…] ignificance of results was assessed using Fisher’s exact test to determine the respective p-value for each class when compared with the entire set of human proteins. In parallel, we used Bioconductor FGNet (version 3.6) [] to build and enable visualization of functional gene networks, generated based on the functional enrichment analyses performed with the inbuilt GeneTerm Linker. […]


R Script Approach to Infer Toxoplasma Infection Mechanisms From Microarrays and Domain Domain Protein Interactions

Bioinform Biol Insights
PMCID: 5753922
PMID: 29317802
DOI: 10.1177/1177932217747256

[…] map into gene symbol. This list is included in Additional file 1.Step 4. Subsequently, functional enrichment analysis (FEA) was performed with the different gene sets obtained from Step 3, using the FGNet enrichment package.Step 5. We included the sqldf package in our R script, as well as the DDI list “INTERACTIONS” to map all domains obtained from the previous host enrichment gene sets (in Step […]


Small Non coding RNA Abundance in Adrenocortical Carcinoma: A Footprint of a Rare Cancer

J Genomics
PMCID: 5607708
PMID: 28943972
DOI: 10.7150/jgen.22060
call_split See protocol

[…] n was performed with MetaCore pathway analysis of differentially expressed genes (Thomson Reuters, New York, NY) using p<0.05 (ACC vs control). Differentially regulated gene lists were used to build functional gene networks and generate disease biomarkers and GO terms (Data analyzed by Gene Arrays, Entity of Vedic Research, Inc., New York, USA). […]


Monocyte derived alveolar macrophages drive lung fibrosis and persist in the lung over the life span

PMCID: 5551573
PMID: 28694385
DOI: 10.1084/jem.20162152

[…] ose involved in lipid metabolic processes and blood microparticle formation (). We performed a functional network analysis of the top 100 differentially expressed genes in cluster III using DAVID and Fgnet tools (; ). This analysis revealed 14 highly overlapping metagroups with a core set of hub genes implicated in fibrotic signaling processes (e.g., Adam8, Arg1, Apoe, Itga6, Mfge8, Mmp12, Mmp13, […]


Exploration of small RNA seq data for small non coding RNAs in Human Colorectal Cancer

J Genomics
PMCID: 5362762
PMID: 28348640
DOI: 10.7150/jgen.18856
call_split See protocol

[…] To investigate biological pathway interactions of small RNA expression, we used MetaCore pathway analysis of differentially expressed genes (Thomson Reuters, New York, NY) , , to delineate functional gene networks. This was based on differentially regulated gene lists with p<0.05 from each group (tumor vs benign, metastasis vs benign, metastasis vs tumor) as input (Data analyzed by Gene […]


A Comprehensive NGS Data Analysis of Differentially Regulated miRNAs, piRNAs, lncRNAs and sn/snoRNAs in Triple Negative Breast Cancer

PMCID: 5370502
PMID: 28367238
DOI: 10.7150/jca.17633
call_split See protocol

[…] nalyzed using MetaCore pathway analysis of differentially expressed genes (Thomson Reuters, New York, NY) with p < 0.05 from each group (TNBC vs adjacent normal tissue; along with different stages). Functional gene networks were built based on differentially regulated gene lists as input to generate disease biomarkers and GO terms (Data analyzed by Gene Arrays, Entity of Vedic Research, Inc., New […]


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FGNet institution(s)
Bioinformatics and Functional Genomics Research Group, Cancer Research Center (Consejo Superior de Investigaciones Científicas, Universidad de Salamanca and Instituto de Investigación Biomédica de Salamanca, CSIC/USAL/IBSAL), Salamanca, Spain

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