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

Omics data for gene sets
  • Microarray: 15,218
  • RNA-seq: 3,660
  • ChIP-seq: 904
  • 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: 2019-07-31

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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