Solanum lycopersicum, the second most important vegetable crop in the world, is also an important model plant for the study of fruit ripening and disease resistance. Abundant germplasm resources and ease of transformation facilitate the first functional characterization of key genes which are involved in ethylene biosynthesis and fruit ripening. However, the function of tomato genes remains largely unknown. Its fruit is an important source of antioxidant compounds, such as lycopene, β-carotene, anthocyanin and ascorbic acid. Among these secondary metabolites (SMs), lycopene and anthocyanin can prevent some diseases and delay aging which benefit to human health. Therefore, it will be of great significance to study the pathways related to SMs biosynthesis in tomato.
About the database
We integrated 343 transcriptome and 136 epigenome data sets to construct co-expression network and define chromatin state, respectively. We identified 4,387 functional modules from global network and two conditional networks with expression view at multi-dimensional levels (development and stress), respectively, which covers diverse functions like secondary metabolite (SM) biosynthesis, pathogen resistance, fruit development and ripening. We added predicted protein-protein interaction (PPI) pairs and miRNA targets into the network. The visualization of chromatin states and association with protein-coding genes and epigenetic marks in genome were shown in UCSC genome browser. Some support analysis tools, such as gene set enrichment analysis (GSEA), module enrichment analysis, cis-element enrichment analysis and ID conversion, were also provided. We hope TomAP platform can help clarify the regulatory mechanism and identify functional genes or modules associated with important agronomic traits.
Contact us
If you have any questions or suggestions, please contact us: sz20193020204@cau.edu.cn and zhensu@cau.edu.cn. If you want to know more about our work, please click here.
Citation
Yaxin Cao, Jiajie She, Zhongqiu Li, Yue Liu, Tian Tian, Qi You, Hengyu Yan, Xuelian Ma, Wenying Xu, ZhenSu. (2023). TomAP: A multi-omics data analysis platform for advancing functional genomics research in tomatoes. New Crops. doi: 10.1016/j.ncrops.2023.10.001. link
News
Links
Sol Genomics Network
Tomato Genetics Resource Center
TFGD
TomatoNET
TOMATOMICS
TomExpress
CoxPathDB
MethBank