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Plant Regulomics: a data-driven interface for retrieving upstream regulators from plant multi-omics data.

Xiaojuan Ran1,2, Fei Zhao1,2, Yuejun Wang1,2

  • 1National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China.

The Plant Journal : for Cell and Molecular Biology
|September 9, 2019
PubMed
Summary
This summary is machine-generated.

Plant Regulomics integrates vast plant omics data to identify gene regulators. This tool aids researchers in understanding gene regulation and biological significance from high-throughput experiments.

Keywords:
Plant Regulomicsdata-driveninterfacetechnical advanceupstream regulators’omics data

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Area of Science:

  • Plant biology
  • Bioinformatics
  • Genomics

Background:

  • High-throughput technologies are crucial for plant research, but interpreting complex 'omics data, especially identifying gene regulators, remains challenging.
  • Existing functional annotation platforms primarily address gene function, leaving a gap in understanding regulatory mechanisms.
  • Understanding gene regulation is essential for a comprehensive view of plant biological processes.

Purpose of the Study:

  • To present Plant Regulomics, a novel interface for integrating and analyzing plant transcriptomic and epigenomic data.
  • To provide a unified statistical framework for mining 'omics data to identify upstream regulators.
  • To facilitate the interpretation of biological significance within high-throughput plant research.

Main Methods:

  • Integration of 19,925 transcriptomic and epigenomic datasets from six plant species.
  • Inclusion of functional evidence, including 58,112 terms and 695,414 protein-protein interactions.
  • Processing of epigenomic data into targeted genomic loci and organization into gene modules and loci lists.
  • Development of a statistical framework to identify upstream factors, treatments, and conditions regulating input gene lists or loci.

Main Results:

  • Plant Regulomics successfully integrates diverse plant 'omics data and functional evidence.
  • The platform enables the retrieval of upstream regulators and experimental conditions for any given gene list or genomic loci.
  • Pair-wise transcriptomic comparisons and epigenomic data processing were performed across multiple plant species.

Conclusions:

  • Plant Regulomics offers a powerful, user-friendly web interface for exploring plant gene regulation.
  • The integrated approach aids in uncovering the biological significance of high-throughput data by identifying regulatory networks.
  • This resource is valuable for advancing plant research by providing insights into gene regulatory mechanisms.