CorNet Arabidopsis

CorNet Arabidopsis enables integration and network analysis of diverse Arabidopsis thaliana datasets to construct co-expression and regulatory networks.

Key Features:

• Data Integration: CORNET 2.0 integrates microarray data, transcription factor (TF) interactions, protein-protein interaction (PPI) data, and gene-gene associations from resources such as AraNet.
• Network Construction: Constructs co-expression and PPI networks centered on multiple input genes or proteins and supports different search options for network generation.
• Functional Annotations: Provides literature retrieval, phenotypes, Plant Ontology terms, and biological pathway annotations for network components.
• Visualization: Utilizes Cytoscape to visualize networks and associated evidence from multiple data types.
• Cross-Species Application: Extends network construction to other crop species, including maize.

Scientific Applications:

• Gene regulation analysis: Identifying regulatory interactions and TF–target relationships in Arabidopsis thaliana.
• Co-expression analysis: Detecting co-expression patterns and modules from integrated microarray and expression datasets.
• Protein interaction mapping: Mapping protein-protein interactions within regulatory networks using integrated PPI data.
• Comparative network studies: Applying network construction to crop species such as maize for cross-species comparison of regulatory networks.

Methodology:

Integration of heterogeneous data sources by leveraging existing databases (e.g., AraNet) and newly identified interactions, combining coexpression analysis with PPI and TF interaction data to construct regulatory networks.