tModBase

tModBase catalogs tRNA modification profiles from 103 datasets generated using second- and third-generation sequencing across ten species and analyzes epitranscriptome signals to identify misincorporation and termination signatures, relate modifications to RNA modification enzymes and 1442 tsRNA expression profiles, and associate modification patterns with 654 DNA variations and transcriptome data from 32 cancers.

Key Features:

• Dataset scope: Analysis across 103 datasets generated using second- and third-generation sequencing technologies.
• Species coverage: Profiles tRNA modifications across ten species.
• Detection signals: Highlights misincorporation and termination signals at tRNA modification sites.
• Tissue and cell-line profiling: Reports modification patterns observed in various tissues and cell lines.
• Cancer transcriptome integration: Integrates transcriptome data from 32 different cancers to summarize disease-linked characteristics.
• tsRNA expression analysis: Provides expression profiles for 1442 tRNA-derived small RNAs (tsRNAs) and explores their relationships with modifications.
• DNA variation analysis: Examines 654 DNA variations in relation to tRNA modification patterns.
• RNA modification enzyme relationships: Explores correlations between tRNA modifications and RNA modification enzyme expression.

Scientific Applications:

• Epitranscriptomic mapping: Comparative mapping of tRNA modification landscapes across species, tissues, and cell lines.
• Modification signature analysis: Identification and characterization of misincorporation and termination sequencing signatures at modification sites.
• Disease association studies: Association of tRNA modification patterns with cancer transcriptomes and other disease-linked characteristics.
• tsRNA research: Investigation of how tRNA modifications relate to expression and potential functions of 1442 tsRNAs.
• Genotype–modification associations: Analysis of 654 DNA variations to assess genetic influences on tRNA modification patterns.

Methodology:

Analysis of 103 second- and third-generation sequencing datasets; detection of misincorporation and termination signals at tRNA modification sites; integration of transcriptome data from 32 cancers; correlation analyses between tRNA modifications, RNA modification enzyme expression, and 1442 tsRNA profiles; and examination of 654 DNA variations.