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

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.

Figure 1. The overall workflow of PoplarGene construction.

PoplarGene network construction included three main steps: (a) inferring functional gene pairs; (b) assigning likelihood ratio scores for network links and (c) integrating component network linkages. The PoplarGene web server was then developed based on network linkages and other related functionalities.

Figure 2. Summary of quality assessment of the PoplarGene network.

(A) The gene linkages derived from 23 diverse functional genomics data sets, representing millions of experimental or computational observations, were integrated into a comprehensive network with higher accuracy and genome coverage than any single data set. The integrated network contains 1,967,631 linkages and 29,049 genes (>70% of the P. trichocarpa coding genome). The x-axis represents the log-scaled coverage of the P. trichocarpa coding genome covered by linkages derived from the corresponding datasets (curves). The y-axis indicates the accuracy of functional linkages, measured as the cumulative log likelihood of linked genes to shared GO-BP term annotations tested using 0.632 bootstrapping and plotted for each bin of 1,000 linkages. The datasets were designated AA-BB, with AA indicating species of data origin (AT, A. thaliana; CE, C. elegans; DM, D. melanogaster; HS, H. sapiens; OS, O. sativa; PT, P. trichocarpa; SC, S. cerevisiae) and BB indicating data type (CC, co-citation; CX, mRNA coexpression; DC, domain co-occurrence; GN, gene neighbor; LC, literature curated protein interactions; HT, high-throughput experimental screening of interaction; PG, phylogenetic profiles). (B) Venn diagram of the gene linkages, indicating that the PoplarGene network contains many more linkages than those derived by orthology transfer from the Arabidopsis gene network AraNet and the rice gene network RiceNet and that they have higher linkage accuracy. Linkage accuracy was measured using an independent set of reference linkages obtained from the agriGO database. (C) Precision-recall analysis comparing the PoplarGene network to the AraNet-derived network and the RiceNet-derived network. (D) Box-and-whisker plot of network predictive power for 277 agriGO BP terms (with more than four annotated genes), as measured by the area under the curve from ROC analysis.

Figure 3. Screenshots of the PoplarGene web service.

Five modules were included in the PoplarGene web service: (A) Neighborhood-based gene priority module; (B) Gene search module; (C) Context-based gene priority module; (D) Interaction transferring module and (E) Gene extensive annotation module. (F) Other tools provided by the PoplarGene web service.

Figure 4. Case studies using PoplarGene.

(A) Validation of new candidate poplar genes for secondary xylem development based on the neighborhood-based gene priority method. (B) Orthology transfer of PoplarGene network linkage to Eucalyptus grandis.