PoplarGene: poplar gene network and resource for mining functional information for genes from woody plants.

Bingyu Zhang,Jiafei Chen,Yanguang Chu,Weixi Zhang,Xiaohua Su,Qi Liu,Qinjun Huang,Changjun Ding

doi:10.1038/srep31356

Bingyu Zhang, Jiafei Chen + Show 6 more

Open Access

https://doi.org/10.1038/srep31356

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Abstract

Poplar is not only an important resource for the production of paper, timber and other wood-based products, but it has also emerged as an ideal model system for studying woody plants. To better understand the biological processes underlying various traits in poplar, e.g., wood development, a comprehensive functional gene interaction network is highly needed. Here, we constructed a genome-wide functional gene network for poplar (covering ~70% of the 41,335 poplar genes) and created the network web service PoplarGene, offering comprehensive functional interactions and extensive poplar gene functional annotations. PoplarGene incorporates two network-based gene prioritization algorithms, neighborhood-based prioritization and context-based prioritization, which can be used to perform gene prioritization in a complementary manner. Furthermore, the co-functional information in PoplarGene can be applied to other woody plant proteomes with high efficiency via orthology transfer. In addition to poplar gene sequences, the webserver also accepts Arabidopsis reference gene as input to guide the search for novel candidate functional genes in PoplarGene. We believe that PoplarGene (http://bioinformatics.caf.ac.cn/PoplarGene and http://124.127.201.25/PoplarGene) will greatly benefit the research community, facilitating studies of poplar and other woody plants.

Highlights

Gene networks increases both network accuracy and coverage by integrating heterogeneous biological data into a single model[15,16]
The PoplarGene network was constructed based on diverse types of large-scale experimental and genomic datasets using machine-learning methods (Fig. 1)
The gold-standard functional gene pairs used for network training were derived from Biological Process of Gene Ontology in Biofuel Feedstock Genomics Resource (BFGR)[23], Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway[24], MapMan Pathway[25] and PoplarCyc pathway[26]

Summary

Introduction

Gene networks increases both network accuracy and coverage by integrating heterogeneous biological data into a single model[15,16] Using this approach, functional associations are determined between genes in a genome based on diverse data sets, each containing millions of individual observations, which are integrated into a comprehensive gene network. Network-guided screening could be performed to identify new candidate genes linked to a specific trait based upon network linkages with previously identified genes associated with these traits. In addition to poplar genes, the webserver accepts Arabidopsis reference genes as input to guide the search for novel candidate functional genes in the PoplarGene network. To the best of our knowledge, PoplarGene is the most comprehensive functional linkage resource for poplar to date. We believe that its user-friendly web interface will be highly beneficial to the research community, representing a valuable resource for better understanding poplar and other woody plants

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Conclusion