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AraNet v2: an improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species.

Lee T, Yang S, Kim E, Ko Y, Hwang S, Shin J, Shim JE, Shim H, Kim H, Kim C, Lee I - Nucleic Acids Res. (2014)

Bottom Line: Recent advances in high-throughput experimental technology have enabled the generation of an unprecedented amount of data from A. thaliana, which has facilitated data-driven approaches to unravel the genetic organization of plant phenotypes.We previously published a description of a genome-scale functional gene network for A. thaliana, AraNet, which was constructed by integrating multiple co-functional gene networks inferred from diverse data types, and we demonstrated the predictive power of this network for complex phenotypes.To enhance the usability of the network, we implemented an AraNet v2 web server, which generates functional predictions for A. thaliana and 27 nonmodel plant species using an orthology-based projection of nonmodel plant genes on the A. thaliana gene network.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea.

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A schematic figure of the two different query processes for the network-assisted hypothesis generation implemented in AraNet v2.
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Figure 2: A schematic figure of the two different query processes for the network-assisted hypothesis generation implemented in AraNet v2.

Mentions: Technical barriers to the investigation of nonmodel plant genomics and genetics have been largely circumvented with the advent of NGS. Plant scientists have started to look beyond the model plant, Arabidopsis, to other nonmodel plant species such as food and energy crops. As of June 2014, the genomes of more than 30 plant species have been fully sequenced. Systems-level functional models such as gene networks, however, are not available for most nonmodel plants due to a lack of genome-scale functional profile data such as gene expression microarray, RNA sequencing, and genome-scale protein–protein interaction analysis. Given that there has not yet been a significant accumulation of species-specific functional genomics data, network construction using an orthology-based transfer of network information from a model plant, A. thaliana, to nonmodel plants may be an effective approach (17–19). Alternatively, genes from a nonmodel plant can be projected onto AraNet v2 by orthology, which would allow for the efficient implementation of a network-assisted functional study of a large volume of nonmodel plant species based on a single gene network. We therefore renovated the AraNet v2 web server to perform functional predictions not only for A. thaliana but also for the 27 nonmodel plant species listed in Supplementary Table 2. Because our published functional network for rice (20) is based on the previous version of AraNet, we have decided to include rice for AraNet v2 server. Users can select one of 28 plant species (A. thaliana or one of the 27 nonmodel plants) and submit a set of query genes to the network search page of the web server. For queries involving nonmodel plant species, the server provides A. thaliana orthologs of the nonmodel plant genes pre-mapped by the best-bidirectional BLASTp hits. This strict orthology was employed to reduce spurious functional inference from prevalent paralogs in plant species. The prediction results show both the original query plant genes and the A. thaliana orthologs. The query process implemented for AraNet v2 is summarized in Figure 2. More detailed descriptions about submission methods and interpretations of query results are available from the tutorial page at www.inetbio.org/aranet/.


AraNet v2: an improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species.

Lee T, Yang S, Kim E, Ko Y, Hwang S, Shin J, Shim JE, Shim H, Kim H, Kim C, Lee I - Nucleic Acids Res. (2014)

A schematic figure of the two different query processes for the network-assisted hypothesis generation implemented in AraNet v2.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383895&req=5

Figure 2: A schematic figure of the two different query processes for the network-assisted hypothesis generation implemented in AraNet v2.
Mentions: Technical barriers to the investigation of nonmodel plant genomics and genetics have been largely circumvented with the advent of NGS. Plant scientists have started to look beyond the model plant, Arabidopsis, to other nonmodel plant species such as food and energy crops. As of June 2014, the genomes of more than 30 plant species have been fully sequenced. Systems-level functional models such as gene networks, however, are not available for most nonmodel plants due to a lack of genome-scale functional profile data such as gene expression microarray, RNA sequencing, and genome-scale protein–protein interaction analysis. Given that there has not yet been a significant accumulation of species-specific functional genomics data, network construction using an orthology-based transfer of network information from a model plant, A. thaliana, to nonmodel plants may be an effective approach (17–19). Alternatively, genes from a nonmodel plant can be projected onto AraNet v2 by orthology, which would allow for the efficient implementation of a network-assisted functional study of a large volume of nonmodel plant species based on a single gene network. We therefore renovated the AraNet v2 web server to perform functional predictions not only for A. thaliana but also for the 27 nonmodel plant species listed in Supplementary Table 2. Because our published functional network for rice (20) is based on the previous version of AraNet, we have decided to include rice for AraNet v2 server. Users can select one of 28 plant species (A. thaliana or one of the 27 nonmodel plants) and submit a set of query genes to the network search page of the web server. For queries involving nonmodel plant species, the server provides A. thaliana orthologs of the nonmodel plant genes pre-mapped by the best-bidirectional BLASTp hits. This strict orthology was employed to reduce spurious functional inference from prevalent paralogs in plant species. The prediction results show both the original query plant genes and the A. thaliana orthologs. The query process implemented for AraNet v2 is summarized in Figure 2. More detailed descriptions about submission methods and interpretations of query results are available from the tutorial page at www.inetbio.org/aranet/.

Bottom Line: Recent advances in high-throughput experimental technology have enabled the generation of an unprecedented amount of data from A. thaliana, which has facilitated data-driven approaches to unravel the genetic organization of plant phenotypes.We previously published a description of a genome-scale functional gene network for A. thaliana, AraNet, which was constructed by integrating multiple co-functional gene networks inferred from diverse data types, and we demonstrated the predictive power of this network for complex phenotypes.To enhance the usability of the network, we implemented an AraNet v2 web server, which generates functional predictions for A. thaliana and 27 nonmodel plant species using an orthology-based projection of nonmodel plant genes on the A. thaliana gene network.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea.

Show MeSH