Pol3Base

Pol3Base catalogs RNA polymerase III (Pol III)-transcribed non-coding RNAs and integrates regulatory, interaction, expression, epitranscriptomic, evolutionary conservation, tRNA-derived small RNA (tsRNA), and somatic mutation data to support functional and disease-associated analyses.

Key Features:

• Regulatory Networks: Contains thousands of regulatory relationships between approximately 79,000 ncRNAs and transcription factors derived from integration of 56 ChIP-seq datasets.
• Protein Interactions: Incorporates CLIP-seq datasets to identify interactions between ncRNAs and over 240 RNA-binding proteins.
• Epitranscriptomic Modifications: Catalogs around 9,700 RNA modifications within thousands of Pol III-transcribed ncRNAs.
• Expression Profiles: Characterizes expression across more than 70 tissues and 28 tumor types.
• Evolutionary Conservation: Provides comparative analysis between human and mouse genomes identifying approximately 4,000 evolutionarily conserved ncRNAs.
• tRNA-Derived Small RNAs (tsRNAs): Identifies around 11,403 tsRNAs across 32 tumor types.
• Mutation Analysis: Analyzes somatic mutation data to generate a mutation map for Pol III-transcribed ncRNAs.

Scientific Applications:

• Gene regulation: Dissects regulatory relationships between Pol III-transcribed ncRNAs and transcription factors using ChIP-seq–derived networks.
• Post-transcriptional modification studies: Enables analysis of epitranscriptomic modification patterns across Pol III-transcribed ncRNAs.
• Evolutionary biology: Supports comparative human–mouse analyses to identify conserved Pol III-transcribed ncRNAs.
• Oncology and disease association: Facilitates investigation of expression profiles, tsRNAs, and somatic mutations of Pol III-transcribed ncRNAs across multiple tumor types.

Methodology:

Integration of 56 ChIP-seq datasets and CLIP-seq datasets, cataloging of RNA modifications, comparative analysis between human and mouse genomes, identification of tsRNAs across tumor types, and analysis of somatic mutation data.