Output - TSB (Transcriptional Strand Bias)
This page provides detailed information about Transcriptional Strand Bias (TSB) output files.
Overview
TSB analysis examines whether mutations show preferential occurrence on the transcribed or untranscribed strand of genes, which can indicate specific mutational processes.
Output Files
| File | # of Sequences | Calculation |
|---|---|---|
| strandBiasTest_24.txt | 24 | 6 × 4 |
| strandBiasTest_384.txt | 384 | 4 × 24 × 4 |
| strandBiasTest_6144.txt | 6144 | 4 × 384 × 4 |
Strand Bias Categories
| Category | Code | Description |
|---|---|---|
| Transcribed | T | Mutation on the transcribed (template) strand |
| Untranscribed | U | Mutation on the untranscribed (coding) strand |
| Non-transcribed | N | Mutation in intergenic region (no transcription) |
| Bidirectional | B | Mutation in region with overlapping transcription |
| Questionable | Q | Ambiguous strand assignment |
Statistical Output
The TSB analysis produces statistical metrics for each mutation type:
Enrichment Values
- Transcribed strand enrichment: Ratio of mutations on transcribed vs untranscribed strand
- Untranscribed strand enrichment: Ratio of mutations on untranscribed vs transcribed strand
Statistical Tests
| Metric | Description |
|---|---|
| p-value | Statistical significance of strand bias |
| q-value (FDR) | False discovery rate corrected p-value |
| Fold enrichment | Magnitude of strand bias |
strandBiasTest_24.txt
Contains strand bias analysis for the 6 basic mutation types across 4 TSB categories.
Format: - Rows: 6 mutation types (C>A, C>G, C>T, T>A, T>C, T>G) - Categories: T, U, N, B
strandBiasTest_384.txt
Extends the analysis to include sequence context (SBS-96 format) with strand bias.
Calculation: 4 (5' context) × 24 × 4 (3' context) = 384 sequences
strandBiasTest_6144.txt
Full extended context analysis with strand bias.
Calculation: 4 × 384 × 4 = 6144 sequences
Interpretation
Transcriptional Strand Bias Patterns
| Pattern | Possible Cause |
|---|---|
| More C>T on transcribed strand | Transcription-coupled repair of UV damage |
| More T>A on untranscribed strand | Adenine damage by certain carcinogens |
| No strand bias | Random/replication-associated mutations |
Biological Significance
Transcriptional strand bias can indicate:
- Transcription-coupled nucleotide excision repair (TC-NER): Preferential repair of bulky lesions on the transcribed strand
- Transcription-associated mutagenesis: Increased mutation rates during transcription
- DNA damage patterns: Certain mutagens preferentially damage specific strands
Usage Notes
- TSB analysis requires
tsb_stat=Trueparameter - Results are most meaningful for samples with sufficient mutation counts
- Consider multiple testing correction when interpreting p-values