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GeneNet specifications

Information


Unique identifier OMICS_12261
Name GeneNet
Software type Toolkit/Suite
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB, Perl
Computer skills Advanced
Stability Stable
Requirements
perl, GeneNet
Maintained Yes

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Versioning


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Maintainer


  • person_outline Avigail Taylor

Publications for GeneNet

GeneNet citations

 (5)
library_books

Whole exome sequencing in obsessive compulsive disorder identifies rare mutations in immunological and neurodevelopmental pathways

2016
PMCID: 4872454
PMID: 27023170
DOI: 10.1038/tp.2016.30

[…] ted edges. We included PPIs that were present in any of the 10 databases consolidated within iRefIndex (). We applied two methods of permutation, ‘seed randomization' and ‘network permutation,' using GeneNet toolbox for MATLAB to show that the connectivity metrics of our network are different from networks generated by chance. […]

library_books

A Systems Genetics Approach and Data Mining Tool to Assist in the Discovery of Genes Underlying Complex Traits in Oryza sativa

2013
PLoS One
PMCID: 3713027
PMID: 23874666
DOI: 10.1371/journal.pone.0068551

[…] study by Zhao et al were used . Genes overlapping both QTL and GWAS SNP intervals were putatively assigned the trait. These associations as well as all GILs were input into an online database called GeneNet Engine which is available online at http://sysbio.genome.clemson.edu. The data is housed in a Chado database schema with custom tables and visualized using Tripal . Next all available rice SN […]

library_books

A metabolomic strategy defines the regulation of lipid content and global metabolism by Δ9 desaturases in Caenorhabditis elegans

2012
BMC Genomics
PMCID: 3398271
PMID: 22264337
DOI: 10.1186/1471-2164-13-36

[…] The fatty acid peaks identified in the GC-FID chromatograms were normalised to the internal standard, imported into R and analysed by Gaussian Graphical Models (GGM), using GeneNet [[]; http://strimmerlab.org/software/genenet/]. […]

library_books

Identification of transcription factor's targets using tissue specific transcriptomic data in Arabidopsis thaliana

2010
BMC Syst Biol
PMCID: 2982689
PMID: 20840729
DOI: 10.1186/1752-0509-4-S2-S2

[…] number of genes is comparable to number of samples in the microarray data [,]. One way to avoid this limitation is to use GGM with regularization and moderation, which is implemented as an R package GeneNet [,]. This method has been used to infer genome-scale regulatory network for A. thaliana transcriptome []. Some other methods are based on probabilistic models, such as the Bayesian network [] […]

library_books

From correlation to causation networks: a simple approximate learning algorithm and its application to high dimensional plant gene expression data

2007
BMC Syst Biol
PMCID: 1995222
PMID: 17683609
DOI: 10.1186/1752-0509-1-37

[…] ion. This graph is very hard to interpret, the branches do not have any immediate or intuitive meaning (a complete annotation of the nodes can be found along with the dataset itself in the R package "GeneNet" []). For instance, there are no hubs as typically observed in biological networks [,].This is in great contrast to the partially directed partial correlation graph. For this specific data set […]

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GeneNet institution(s)
MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK; The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
GeneNet funding source(s)
This work was supported by the Medical Research Council; the Wellcome Trust [093941/Z/10/Z], [090532/Z/09/Z] (The Wellcome Trust Centre for Human Genetics); the European Union’s Seventh Framework Programme project GENCODYS [241995]; and Somerville-Clarendon and Natural Sciences and Engineering Research Council of Canada Scholarships.

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