Inference of plant gene regulatory networks using data-driven methods: A practical overview
Shubhada R Kulkarni1, Klaas Vandepoele1
1Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052 Ghent, Belgium.
Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms
|November 4, 2019
Summary
This review surveys tools for analyzing plant gene regulatory networks (GRNs). It categorizes platforms for promoter motif and network analysis to understand gene regulation in Arabidopsis.
Area of Science:
- Plant molecular biology
- Genomics
- Bioinformatics
Background:
- Transcriptional regulation governs plant growth and development via transcription factors (TFs) and gene regulatory networks (GRNs).
- Understanding GRNs is crucial for deciphering plant cell function and gene regulation across diverse conditions.
- Despite progress, a comprehensive overview of plant GRN analysis platforms is lacking.
Purpose of the Study:
- To review and categorize existing databases, platforms, and tools for data-driven analysis of plant gene regulation.
- To provide an overview of resources for analyzing gene regulatory networks in Arabidopsis.
- To highlight the strengths and limitations of current GRN analysis approaches.
Main Methods:
- Literature review of computational and experimental approaches for GRN identification.
- Categorization of platforms into promoter motif analysis tools and network analysis tools.
- Discussion of integrated datasets, platform functionalities, and analytical methodologies.
Main Results:
- Identified and categorized tools for promoter motif analysis (motif mapping) and network analysis (identifying regulators and generating GRNs).
- Evaluated diverse datasets and highlighted the strengths and weaknesses of various platforms for plant GRN analysis.
- Discussed limitations of current approaches, emphasizing the need for integrative strategies.
Conclusions:
- Current platforms offer valuable resources for plant GRN analysis, but limitations exist.
- Further development requires integrative approaches to fully unravel complex gene regulatory networks in plants.
- This review serves as a guide to available tools for plant gene regulation research.
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