MetaNetwork statistics

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Citations per year

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

This map represents all the scientific publications referring to MetaNetwork per scientific context
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Protocols

MetaNetwork specifications

Information


Unique identifier OMICS_32412
Name MetaNetwork
Software type Application/Script
Interface Command line interface
Restrictions to use None
Output data All relevant information such as the estimated effect of each mQTL.
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability No
Maintained No

Versioning


No version available

Maintainer


This tool is not available anymore.

Publication for MetaNetwork

MetaNetwork citations

 (6)
library_books

Review of Statistical Learning Methods in Integrated Omics Studies (An Integrated Information Science)

2018
Bioinform Biol Insights
PMCID: 5824897
PMID: 29497285
DOI: 10.1177/1177932218759292

[…] nd a permutation test is proposed by the author to determine the metabolite/protein/RNA significance for predicting the trait. Second, the integrated linkage map is used and implemented via R package metanetwork. Finally, the final selected gene, protein, and metabolites including the trait are used to construct the network. The network’s nodes are formed by the aforementioned molecules and traits […]

library_books

“Every Gene Is Everywhere but the Environment Selects”: Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis

2016
Genome Biol Evol
PMCID: 4898794
PMID: 27190206
DOI: 10.1093/gbe/evw077

[…] an 1,500 bp). These were used as input for homology-based network construction pipeline. Fasta files and scripts used in this work have been made publicly available at http://sourceforge.net/projects/metanetwork/. […]

library_books

Regulatory Network of Secondary Metabolism in Brassica rapa: Insight into the Glucosinolate Pathway

2014
PLoS One
PMCID: 4164526
PMID: 25222144
DOI: 10.1371/journal.pone.0107123

[…] re calculated using an MQM procedure . The output of the transcriptional data of the candidate regulatory genes (eQTLs) was filtered for a LOD threshold value of >3.5. The data was analyzed using the MetaNetwork computational protocol as described in to obtain second order correlation values. The generated files were plotted using Cytoscape . […]

library_books

Multiple monoaminergic modulation of posturo locomotor network activity in the newborn rat spinal cord

2014
Front Neural Circuits
PMCID: 4133733
PMID: 25177275
DOI: 10.3389/fncir.2014.00099

[…] rts such persistent actions.When considering the integrated functioning of hindlimb and axial networks involved in dynamic posture, a different perspective is required since as we demonstrate, this <<metanetwork>> can be configured into various functional states according to the neuromodulatory environment. As shown in Figures and , although the amines and EAAs have a qualitatively cumulative eff […]

call_split

Genetic analysis of metabolites in apple fruits indicates an mQTL hotspot for phenolic compounds on linkage group 16

2012
J Exp Bot
PMCID: 3350913
PMID: 22330898
DOI: 10.1093/jxb/err464
call_split See protocol

[…] (SSR), and random amplified polymorphic DNA (RAPD) markers, and some isozymes ().In the untargeted mQTL mapping of metabolites in apple, the individual maps of ‘Prima’ and ‘Fiesta’ were used, as the MetaNetwork could not incorporate the integrated map of cross-pollinating crops such as apple. In the targeted mQTL mapping using MapQTL® 6.0, an integrated map of both parents was constructed and use […]

library_books

A new computational method to split large biochemical networks into coherent subnets

2011
BMC Syst Biol
PMCID: 3045323
PMID: 21294924
DOI: 10.1186/1752-0509-5-25

[…] r: while the subnets are simple, their interconnections reconstitute exactly the original network. This suggests that to judge overall effectiveness, the subnets should be considered together with a "metanetwork" which is derived from the original network by contracting the internal nodes of each subnetwork to a single meta-node. It should then be possible to construct a measure that evaluates to […]


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MetaNetwork institution(s)
Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands; Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands; Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
MetaNetwork funding source(s)
Supported by grants from the Netherlands Organization for Scientific Research Program Genomics (050-10-029).

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