G4Atlas

G4Atlas provides a comprehensive transcriptome-wide database of RNA G-quadruplexes (rG4s), tertiary RNA motifs formed by guanine bases pairing through Hoogsteen and Watson-Crick hydrogen bonds, to enable analysis of rG4 formation and their roles in post-transcriptional regulation of gene expression.

Key Features:

• Transcriptome-wide coverage: Includes rG4 data across whole transcriptomes incorporating experimental results from multiple species and conditions.
• Data compilation and classification: Compiles and classifies rG4 entries derived from diverse experimental techniques.
• Experimental techniques: Integrates data generated by rG4-seq, chemical profiling, and ligand-binding methods.
• Dataset scope: Contains results from 82 experimental treatments across 238 samples spanning ten species.
• RNA secondary structure prediction: Provides RNA secondary structure predictions for both identified and unidentified rG4s to assess potential competitive folding scenarios.
• In vitro and in vivo identification: Aggregates rG4 identifications reported from both in vitro and in vivo experimental conditions.

Scientific Applications:

• Exploration of biological functions: Enables investigation of rG4 roles in diverse biological contexts and their potential regulatory impacts on gene expression.
• Support for computational modeling: Provides a data foundation for data-driven deep learning and other computational analyses of rG4 structural features and functional implications.
• Comparative and hypothesis-driven studies: Facilitates comparative transcriptome analyses and generation of hypotheses about rG4 biological significance across species and conditions.

Methodology:

Integrates experimental datasets from rG4-seq, chemical profiling, and ligand-binding assays and includes RNA secondary structure prediction to assess rG4 formation.