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AraNet specifications

Information


Unique identifier OMICS_27253
Name AraNet
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Version 2
Maintained Yes

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana

Maintainer


  • person_outline Insuk Lee

Additional information


http://www.functionalnet.org/aranet/

Publications for AraNet

AraNet citations

 (21)
library_books

araGWAB: Network based boosting of genome wide association studies in Arabidopsis thaliana

2018
Sci Rep
PMCID: 5811503
PMID: 29440686
DOI: 10.1038/s41598-018-21301-4

[…] 1 to calculate the P-values. The effectiveness of network boosting is significantly influenced by the quality of the co-functional gene network. For network boosting, we applied the latest version of AraNet (version 2), which is known as the most accurate and comprehensive co-functional gene network of genes for A. thaliana.To assess the performance of network boosting, we utilized reference pheno […]

library_books

A Meta Analysis Based Method for Prioritizing Candidate Genes Involved in a Pre specific Function

2016
Front Plant Sci
PMCID: 5156684
PMID: 28018423
DOI: 10.3389/fpls.2016.01914

[…] pplied to rank the remaining 26 968 genes annotated in the TAIR10 database (Table ). Further, network analysis revealed that the top 20 ranked genes connect with 150 known flowering-time genes in the AraNet v2 system, resulting in the generation of a hierarchical network that contains three modules and 418 functional associations (Figure ; Table ). This result indicates that the top 20 candidates […]

call_split

Evolutionary interplay between sister cytochrome P450 genes shapes plasticity in plant metabolism

2016
Nat Commun
PMCID: 5059761
PMID: 27713409
DOI: 10.1038/ncomms13026
call_split See protocol

[…] st treated with ethanol:acetic acid (v/v) for 4 h, and then restored in Hoyer's medium before microsopy analysis.Gene co-expression network analysis was performed with the PlaNet on line tool (http://aranet.mpimp-golm.mpg.de/) using At1g74540 (CYP98A8) and At1g74550 (CYP98A9) as gene id inputs. The gene list corresponding to the different co-expression networks (see ) were then subjected to hierar […]

library_books

Learning from Co expression Networks: Possibilities and Challenges

2016
Front Plant Sci
PMCID: 4825623
PMID: 27092161
DOI: 10.3389/fpls.2016.00444

[…] tions, correlations, physical interactions and shared protein domains) to display all predicted interactions for a query gene list in an interactive network. The probabilistic functional gene network AraNet (Lee et al., ) provides a measure to assess the connectivity of the query genes used in regard to the generated network. Additionally, AraNet integrates enrichment analysis tools for network co […]

library_books

Translational genomics for plant breeding with the genome sequence explosion

2015
Plant Biotechnol J
PMCID: 5042036
PMID: 26269219
DOI: 10.1111/pbi.12449

[…] ddition to various accumulated experimental data, RNA‐sequencing data that produce a massive amount of co‐expression data in the public have been shown to significantly increase the prediction power. AraNet, a genomewide gene network for Arabidopsis thaliana, was constructed to predict reliable gene annotation towards plant traits (Lee et al., ). In addition, the network modelling was performed to […]

library_books

'PP2C7s', Genes Most Highly Elaborated in Photosynthetic Organisms, Reveal the Bacterial Origin and Stepwise Evolution of PPM/PP2C Protein Phosphatases

2015
PLoS One
PMCID: 4524716
PMID: 26241330
DOI: 10.1371/journal.pone.0132863

[…] Plant gene expression data were accessed at PlaNet ([]; http://aranet.mpimp-golm.mpg.de/) and Genevisible/Genevestigator ([]; http://genevisible.com/search). Additional data for maize PP2C7 genes were obtained from [] and for rice PP2C7 genes from [], and from Ri […]

Citations

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AraNet institution(s)
Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea; Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, TX, USA
AraNet funding source(s)
Supported by grants from the National Research Foundation of Korea (2015R1A2A1A15055859, 2012M3A9B4 028641, 2012M3A9C7050151).

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