| URL: | http://bioinformatics.cau.edu.cn/croFGD |
| Full name: | Catharanthus roseus Functional Genomics Database |
| Description: | Catharanthus roseus (L.) G. Don, a medicinal plant, produces monoterpene indole alkaloids (MIAs) derived from secologanin and tryptamine. By integrating genome sequence and 76 RNA-seq datasets available in public platforms, we constructed three types of co-expression network, and identified 6,336 functional modules in total. |
| Year founded: | 2019 |
| Last update: | |
| Version: | |
| Accessibility: |
Accessible
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| Country/Region: | China |
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| University/Institution: | China Agricultural University |
| Address: | State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China |
| City: | Beijing |
| Province/State: | Beijing |
| Country/Region: | China |
| Contact name (PI/Team): | Zhen Su |
| Contact email (PI/Helpdesk): | zhensu@cau.edu.cn |
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croFGD: Functional Genomics Database. [PMID: 30967897]
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. |