PlantCircNet

PlantCircNet provides an integrated database and visualization of circular RNA (circRNA)-mediated regulatory networks across eight model plant species to support analysis of circRNA–miRNA–mRNA interactions and functional inference.

Key Features:

• Regulatory Network Visualization: Visualized circRNA–miRNA–mRNA regulatory networks across eight model plant species.
• Comprehensive Data Integration: Integration of circRNA genomic annotations, sequences, and isoforms from multiple sources.
• Search and Sequence Query: Searchable interactions involving specific circRNAs, miRNAs, or mRNAs and support for sequence-based searches.
• Enrichment Analysis: Gene Ontology (GO) enrichment analysis to identify significantly overrepresented GO categories among miRNA targets.
• Example Networks and Biological Contexts: Inclusion of specific networks and examples such as miR156a and AT5G59720 and contexts including flower development and responses to environmental stress.

Scientific Applications:

• Functional inference of circRNAs: Support for identifying circRNAs acting as competing endogenous RNAs (ceRNAs) that modulate miRNA activity.
• Regulatory network analysis: Exploration and characterization of circRNA–miRNA–mRNA regulatory relationships.
• Functional enrichment interpretation: Use of GO enrichment of miRNA targets to infer biological processes associated with circRNA networks.
• Development and stress biology: Investigation of circRNA roles in flower development and plant responses to environmental stress.
• Hypothesis generation and experimental prioritization: Prioritization of candidate circRNA–miRNA–mRNA interactions for experimental validation.

Methodology:

Integration of circRNA genomic annotations, sequences and isoforms from multiple sources, construction and visualization of circRNA–miRNA–mRNA regulatory networks, sequence-based search of circRNAs, and Gene Ontology enrichment analysis for miRNA targets.