BarleyNet: A Network-Based Functional Omics Analysis Server for Cultivated Barley, Hordeum vulgare L

Frontiers in Plant Science
Sungho LeeInsuk Lee

Abstract

Cultivated barley (Hordeum vulgare L.) is one of the most produced cereal crops worldwide after maize, bread wheat, and rice. Barley is an important crop species not only as a food source, but also in plant genetics because it harbors numerous stress response alleles in its genome that can be exploited for crop engineering. However, the functional annotation of its genome is relatively poor compared with other major crops. Moreover, bioinformatics tools for system-wide analyses of omics data from barley are not yet available. We have thus developed BarleyNet, a co-functional network of 26,145 barley genes, along with a web server for network-based predictions (http://www.inetbio.org/barleynet). We demonstrated that BarleyNet's prediction of biological processes is more accurate than that of an existing barley gene network. We implemented three complementary network-based algorithms for prioritizing genes or functional concepts to study genetic components of complex traits such as environmental stress responses: (i) a pathway-centric search for candidate genes of pathways or complex traits; (ii) a gene-centric search to infer novel functional concepts for genes; and (iii) a context-centric search for novel genes associated with ...Continue Reading

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Citations

May 1, 2021·International Journal of Molecular Sciences·Marta PuchtaMaja Boczkowska

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Datasets Mentioned

BETA
GPL1340

Methods Mentioned

BETA
dissection
RNA-seq
Phylogenetic Profile
phylogenetic profiles
environmental stress

Software Mentioned

BarleyNet
RiceNet
DIAMOND
DanioNet
HumanNet
MouseNet
AraNet
MAS5
BLASTP
Ensembl

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