sfgd a comprehensive platform for mining functional information from soybean transcriptome data and its use in identifying acyl-lipid metabolism pathways：安全设备的综合平台从大豆转录组数据和识别酰基脂质代谢途径使用挖掘功能信息.pdf

Yu et al. BMC Genomics 2014, 15:271 /1471-2164/15/271 DATABASE Open Access SFGD: a comprehensive platform for mining functional information from soybean transcriptome data and its use in identifying acyl-lipid metabolism pathways † † * * Juan Yu , Zhenhai Zhang , Jiangang Wei, Yi Ling, Wenying Xu and Zhen Su Abstract Background: Soybean (Glycine max L.) is one of the world’s most important leguminous crops producing high- quality protein and oil. Increasing the relative oil concentration in soybean seeds is many researchers’ goal, but a complete analysis platform of functional annotation for the genes involved in the soybean acyl-lipid pathway is still lacking. Following the success of soybean whole-genome sequencing, functional annotation has become a major challenge for the scientific community. Whole-genome transcriptome analysis is a powerful way to predict genes with biological functions. It is essential to build a comprehensive analysis platform for integrating soybean whole-genome sequencing data, the available transcriptome data and protein information. This platform could also be used to identify acyl-lipid metabolism pathways. Description: In this study, we describe our construction of the Soybean Functional Genomics Database (SFGD) using Generic Genome Browser (Gbrowse) as the core platform. We integrated microarray expression profiling with 255 samples from 14 groups’ experiments and mRNA-seq data with 30 samples from four groups’ experiments, including spatial and temporal transcriptome data for different soybean development stages and environmental stresses. The SFGD includes a gene co-expression regulatory network containing 23,267 genes and 1873 miRNA-target pairs, and a group of acyl