Overview

Plant Regulomics is a data-driven interface for retrieving upstream regulators from plant multi-omics data, which integrates 20,737 transcriptomic and epigenomic data sets and diverse sources of functional evidence (58,112 functional terms and 695,414 protein-protein interactions) from six plant species, namely Arabidopsis thaliana, Oryza sativa, Zea mays, Glycine max, Solanum lycopersicum and Triticum aestivum, along with the orthologous genes from 56 whole-genome sequenced plant species. These data were well-organized to gene modules and further implemented into the same statistical framework.

For any input gene list or genomic loci, Plant Regulomics retrieves the factors, treatments, and experimental/environmental conditions regulating the input from the integrated omics data. Additionally, multiple tools and an interactive visualization are available through a user-friendly web interface.

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Summary

News~:
The data is being added. Please forgive me if there is a problem with some functions of the new species.
Update Protein-protein interactions:6 species[2021-6-1]
Update Chip-Seq:36 species[2021-3-20]
Update GO:42 species[21/1/1]
Update KEGG:42 species[20/12/20]
Update InterPro:42 species[20/12/05]
Update ChIP-Seq:29 species[20/9/30]
Update ChIP-Seq:12 species[20/7/1]
Omics data for gene sets
  • Microarray: 15,218
  • RNA-seq: 3,660
  • ChIP-seq: 10273
  • DAP-seq: 812
  • ChIP-chip: 4
    • Omics data for tissue specificity
  • 165 RNA-seq samples from five plant species including Arabidopsis thaliana, Oryza sativa, Zea mays, Solanum lycopersicum and Triticum aestivum.
    • Motif
  • 489 motifs downloaded from JASPAR.
    • Ortholog
  • 8,463,126 orthologous gene pairs downloaded from Phytozome12.
    • Protein-protein interactions
  • Arabidopsis thaliana: 109,972
  • Oryza sativa: 555,831
  • Zea mays: 29,611
    • Functional konwledgebase
  • GO: 26,226
  • KEGG: 635
  • InterPro: 31,251
    • Last Update: 2021-07-09

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    Citation: Xiaojuan Ran#, Fei Zhao#, Yuejun Wang#, Jian Liu, Yili Zhuang, Luhuan Ye, Meifang Qi, Jingfei Cheng and Yijing Zhang*. (2019), Plant Regulomics: A Data-driven Interface for Retrieving Upstream Regulators from Plant Multi-omics Data[J]. The Plant Journal. doi: 10.1111/tpj.14526





    Plant Regulomics | Develop by Plant Bioinformatics and Functional Epigenomics Group, SIPPE, CAS