AraNet
is a probabilistic functional gene network for Arabidopsis thaliana, which is a model plant organism that has been studied intensively for several decades. Recent advances in omics technology have enabled the generation of an unprecedented amount of data from A. thaliana allowing data-driven approaches to unravel complex gene-to-phenotype association in plants. We previously published a genome-scale functional gene network for A. thaliana, AraNet, by probabilistic integration of heterogeneous omics-data. Nature Biotechnology 2010
The previous version of AraNet is availabe here
AraNet v2
is an improved version of AraNet by incorporating new large-scale experimental data and improved data analysis algorithms. Since the initial development of AraNet, a large volume of new microarray data derived from diverse biological contexts has been added to the publicly available databases. We have also continued to improve machine learning algorithms to infer co-functional links from genomics data. AraNet v2 now covers 84% of A. thaliana coding genomes by TAIR10 with higher accuracy.
Arabidopsis and 28 non-model plant organisms
can be studied using AraNet v2 web server now. We implemented AraNet v2 web server to generate functional predictions for A. thaliana and 28 other non-model plant organisms using an orthology-based projection of non-model plant genes on AraNet. AraNet v2 now provides ‘Find new members of a pathway’ and ‘Infer functions from network neighbors’ network-search options not only for A. thaliana but also for 28 non-model plants organisms. For example, we have projected 17 maize genes associated with leaf initiation on AraNet v2. The projected maize genes were interconnected in AraNet v2, indicating that a pathway for maize leaf initiation is conserved in A. thaliana. Thus, we prioritized additional maize genes for leaf initiation by guilt-by-association using AraNet v2. We observed a significantly higher range of expression levels for the candidate genes in leaf tissues compared to non-leaf tissues.
How to cite AraNet
AraNet v2 : An improved database of co-functional gene networks for study of Arabidopsis thaliana and 27 other non-model plant species. Nucl. Acids Res. 43(D1):D996-D1002,28 January, 2015 (link)
Contact information
Insuk Lee (insuklee (at) yonsei.ac.kr)
Licensing
Contents of this database are freely available for academia and public entities. If you are a commercial entity, please send an email for further information about licensing.
Updates
2015.09.08 Added new plant species : Spirodela polyrhiza. Total 28 non-model plant species are available.
2014.12.04 Extended the maximum number of query genes to 500 in "Find new members of a pathway" option.
2014.11.08 Provided the ortholog relationships between Arabidopsis thaliana and other plant species in Network-download page.
2014.09.15 AraNet v2 website launched.
Funding
This work was supported by the National Research Foundation of Korea grant (2010-0017649) and the Next-Generation BioGreen 21 Program grant (SSAC, PJ009029).