Output TSB

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

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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

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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

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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

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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

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strandBiasTest_6144.txt

Full extended context analysis with strand bias.

Calculation: 4 × 384 × 4 = 6144 sequences

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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:

1. Transcription-coupled nucleotide excision repair (TC-NER): Preferential repair of bulky lesions on the transcribed strand
2. Transcription-associated mutagenesis: Increased mutation rates during transcription
3. DNA damage patterns: Certain mutagens preferentially damage specific strands

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Usage Notes

• TSB analysis requires tsb_stat=True parameter
• Results are most meaningful for samples with sufficient mutation counts
• Consider multiple testing correction when interpreting p-values