She Jiajie, Yan Hengyu, Yang Jiaotong, Xu Wenying, Su Zhen
State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China.
Front Genet. 2019 Mar 22;10:238. doi: 10.3389/fgene.2019.00238. eCollection 2019.
is a medicinal plant, which can produce monoterpene indole alkaloid (MIA) metabolites with biological activity and is rich in vinblastine and vincristine. With release of the scaffolded genome sequence of , it is necessary to annotate gene functions on the whole-genome level. Recently, 53 RNA-seq datasets are available in public with different tissues (flower, root, leaf, seedling, and shoot) and different treatments (MeJA, PnWB infection and yeast elicitor). We used in-house data process pipeline with the combination of PCC and MR algorithms to construct a co-expression network exploring multi-dimensional gene expression (global, tissue preferential, and treat response) through multi-layered approaches. In the meanwhile, we added miRNA-target pairs, predicted PPI pairs into the network and provided several tools such as gene set enrichment analysis, functional module enrichment analysis, and motif analysis for functional prediction of the co-expression genes. Finally, we have constructed an online croFGD database (http://bioinformatics.cau.edu.cn/croFGD/). We hope croFGD can help the communities to study the functional genomics and make novel discoveries about key genes involved in some important biological processes.
是一种药用植物，能够产生具有生物活性的单萜吲哚生物碱（MIA）代谢产物，且富含长春碱和长春新碱。随着其支架基因组序列的发布，有必要在全基因组水平上注释基因功能。最近，公开了53个不同组织（花、根、叶、幼苗和茎）以及不同处理（茉莉酸甲酯、香蕉枯萎病菌感染和酵母激发子）的RNA测序数据集。我们使用内部数据处理流程结合皮尔逊相关系数（PCC）和互信息（MR）算法，通过多层方法构建共表达网络，以探索多维度基因表达（全局、组织偏好和处理响应）。同时，我们将miRNA-靶标对、预测的蛋白质-蛋白质相互作用（PPI）对添加到网络中，并提供了诸如基因集富集分析、功能模块富集分析和基序分析等工具，用于对共表达基因进行功能预测。最后，我们构建了一个在线数据库croFGD（http://bioinformatics.cau.edu.cn/croFGD/）。我们希望croFGD能够帮助相关群体研究功能基因组学，并在参与某些重要生物学过程的关键基因方面取得新发现。
