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

• DOI: 10.1038/srep31356
• Publication Date: 2016-08-12T09:23:13Z
• Authors: Qi Liu; Changjun Ding; Yanguang Chu; Jiafei Chen; Weixi Zhang; Bingyu Zhang; Qinjun Huang; Xiaohua Su
• Keywords: 0301 basic medicine; Internet; 0303 health sciences; Computational Biology; 15. Life on land; Genes, Plant; Article; 03 medical and health sciences; Populus; Gene Expression Regulation, Plant; Databases, Genetic; Data Mining; Gene Regulatory Networks; Algorithms

AbstractPoplar 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/PoplarGeneandhttp://124.127.201.25/PoplarGene) will greatly benefit the research community, facilitating studies of poplar and other woody plants.