isoform-switching

name	isoform-switching
description	Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt rule, ORF disruption, protein domain loss/gain, signal peptide changes, IDR alterations, coding-potential shifts). Tools include IsoformSwitchAnalyzeR v2 (auto-selects satuRn for >5 reps else DEXSeq), the manual DRIMSeq -> DEXSeq/satuRn -> stageR DTU pipeline, and fishpond/swish for inferential-uncertainty-aware DTE. Distinguishes DTU from DGE and DTE; integrates external annotators (CPC2, Pfam, SignalP, IUPred2A or DeepTMHMM). Use when investigating how splicing differences alter protein function or trigger NMD-mediated degradation.
tool_type	r
primary_tool	IsoformSwitchAnalyzeR

Version Compatibility

Reference examples tested with: IsoformSwitchAnalyzeR 2.11+, DRIMSeq 1.34+, DEXSeq 1.52+, satuRn 1.14+, stageR 1.28+, fishpond 2.14+, tximport 1.34+, tximeta 1.24+, Salmon 1.10+

Before using code patterns, verify installed versions match. If versions differ:

• R: packageVersion('<pkg>') then ?function_name to verify parameters
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Isoform Switching and Differential Transcript Usage

Identify shifts in which transcript a gene predominantly uses between conditions, and predict functional consequences. Statistically distinct from DGE and DTE; biologically distinct because the same gene-level expression can hide a complete isoform switch with major protein-level consequences.

DGE vs DTE vs DTU: Which Question Is Being Asked?

Question	Statistic	Tool	Example claim
DGE Does the gene total change?	Sum of transcript counts	DESeq2, edgeR, limma-voom	"Gene X is upregulated 2-fold"
DTE Does this transcript change in absolute abundance?	Per-transcript count	swish (fishpond), DESeq2 on transcripts, sleuth	"Transcript X-201 is upregulated 2-fold"
DTU Do proportions of transcripts within the gene shift?	Vector of per-transcript proportions	DRIMSeq, DEXSeq, satuRn (+ stageR)	"Gene X switches from isoform 201 (50% -> 10%) to 202 (50% -> 90%)"

DTU is statistically harder than DGE because:

1. The null is compositional (proportions sum to 1; one transcript up means another down).
2. Multi-stage testing is required: gene-level "any DTU" + transcript-level "which transcript" -> stageR formalizes this.
3. Quantification uncertainty propagates when transcripts are similar (Salmon EM ambiguity).

DTU and event-level differential splicing answer related but distinct questions: rMATS' IncLevelDifference is essentially a 1-D projection of a DTU shift onto a single event coordinate. The pragmatic 2026 default: run both an event-level tool (rMATS or leafcutter) and a DTU pipeline; reconcile.

Tool Selection for DTU

Tool	Model	When to use	Fails when
IsoformSwitchAnalyzeR v2	Wraps DEXSeq or satuRn + functional consequence annotation	Standard interpretation workflow with NMD/domain output	Manual DTU control needed; very large cohorts (>200)
DRIMSeq	Dirichlet-multinomial on transcript counts; gene-level DTU	Pre-filter step before DEXSeq/satuRn	Cannot annotate functional consequences alone
DEXSeq	Negative-binomial GLM on exon-bin or transcript counts	Classic DTU; conservative; <=5 replicates per condition	Slow at scale; uses bins not transcripts in default mode
satuRn	Quasi-binomial GLM with empirical-Bayes shrinkage	DTU at scale (single-cell, large bulk cohorts)	Newer; less battle-tested than DEXSeq
swish (fishpond)	Non-parametric SAMseq across Salmon Gibbs samples	DTE/DGE incorporating quantification uncertainty	Requires Gibbs samples; not strictly DTU
stageR	Two-stage testing framework	Required for proper OFDR control on top of DRIMSeq/DEXSeq/satuRn	Standalone — wraps another tool's output
sleuth	Bootstrap-based DTE on kallisto	When committed to kallisto pipeline	Less active development; superseded by fishpond+swish

The IsoformSwitchAnalyzeR v2 default rule is: satuRn if any condition has >5 replicates; else DEXSeq. For exactly 5 replicates per condition (boundary), explicitly choose; results may differ.

Decision Tree by Research Question

Question	Recommended approach
Functional consequences of switches (domains, NMD, signal peptide)	IsoformSwitchAnalyzeR v2 with full external annotator pipeline
Pure statistical DTU (gene-level + transcript-level OFDR)	DRIMSeq (filter) -> DEXSeq -> stageR; or -> satuRn -> stageR for n>5
DTU with proper quantification uncertainty	Salmon --numGibbsSamples 20 -> tximeta -> swish for DTE; concurrent DTU
Single-cell DTU	satuRn (DEXSeq doesn't scale to scRNA-seq)
Long-read DTU (PacBio Iso-Seq, ONT)	IsoformSwitchAnalyzeR v2 long-read input mode (no Salmon EM uncertainty)
Time-course DTU	DEXSeq with time as factor + interaction; or limma::lmFit on logit-prop matrix
Cancer / disease — switch hits -> mechanism	Standard pipeline + cross-reference with eCLIP, ClinVar, COSMIC
Therapeutic ASO target identification	Standard pipeline + sashimi visualization + SpliceAI design

IsoformSwitchAnalyzeR v2 Workflow

Goal: Identify isoform switches with functional consequences in one integrated workflow.

Approach: Import Salmon, pre-filter, run statistical test (satuRn auto-selected if any condition has >5 replicates, else DEXSeq), annotate switches with external tools (CPC2, Pfam, SignalP, IUPred2A or DeepTMHMM), then summarize consequences.

library(IsoformSwitchAnalyzeR)

salmonQuant <- importIsoformExpression(
    parentDir = 'salmon_quant/',
    addIsofomIdAsColumn = TRUE
)

design <- data.frame(
    sampleID = colnames(salmonQuant$counts)[-1],
    condition = c('control', 'control', 'control', 'treatment', 'treatment', 'treatment')
)

aSwitchList <- importRdata(
    isoformCountMatrix = salmonQuant$counts,
    isoformRepExpression = salmonQuant$abundance,
    designMatrix = design,
    isoformExonAnnoation = 'annotation.gtf',
    isoformNtFasta = 'transcripts.fa',
    showProgress  


aSwitchList  preFilter
    aSwitchList
    geneExpressionCutoff  
    isoformExpressionCutoff  
    IFcutoff  
    removeSingleIsoformGenes  
    keepIsoformInAllConditions  


aSwitchList  isoformSwitchTestSatuRn
    aSwitchList
    reduceToSwitchingGenes  
    alpha  
    dIFcutoff  

preFilter parameters:

• geneExpressionCutoff = 1 — minimum TPM for gene to be tested (raise for stricter)
• isoformExpressionCutoff = 0 — minimum TPM per isoform (set to 1 for stricter)
• IFcutoff = 0.01 — minimum isoform fraction; below = noise
• removeSingleIsoformGenes = TRUE — drop genes with only one detectable isoform (cannot have DTU)
• keepIsoformInAllConditions = TRUE — require expression across all conditions

For long-read input, use importRdata with long-read transcript counts directly — bypasses Salmon EM uncertainty entirely.

Functional Consequence Annotation

Goal: Predict how each switch alters protein structure, function, and stability.

Approach: Extract sequences, run external annotators outside R, then re-import results into the switchAnalyzeRlist.

aSwitchList <- extractSequence(
    aSwitchList,
    pathToOutput = 'sequences/',
    writeToFile = TRUE
)

# Run external tools on sequences/isoformSwitchAnalyzeR_isoform_*.fasta
# Then import:

# IMPORTANT: ORF analysis must run BEFORE analyzeSwitchConsequences for NMD_status,
# ORF_seq_similarity, and coding_potential consequences to be computed.
aSwitchList <- analyzeORF(aSwitchList, orfMethod = 'longest', genomeObject = NULL)

aSwitchList <- analyzeCPC2(aSwitchList, pathToCPC2resultFile = 'cpc2_results.txt', removeNoncodinORFs = TRUE)
aSwitchList <- analyzePFAM(aSwitchList, pathToPFAMresultFile = 'pfam_results.txt')
aSwitchList <- analyzeSignalP(aSwitchList, pathToSignalPresultFile = 'signalp_results.txt')
aSwitchList <- analyzeIUPred2A(aSwitchList, pathToIUPred2AresultFile = 'iupred2_results.txt'
aSwitchList  analyzeAlternativeSplicingaSwitchList onlySwitchingGenes  

aSwitchList  analyzeSwitchConsequences
    aSwitchList
    consequencesToAnalyze  
        
        
        
        
        
        
        
        
    
    dIFcutoff  

External tool	Purpose	Required for
CPC2 (Coding Potential Calculator 2)	Coding vs non-coding classification	coding_potential consequence
Pfam (HMMER hmmscan against Pfam-A)	Protein domain identification	domains_identified
SignalP 6.0+	Signal peptide prediction	signal_peptide_identified
IUPred2A or DeepTMHMM	Intrinsic disorder regions / TM domains	IDR_identified, IDR_type
NetSurfP-3	Surface accessibility (optional)	Extended IDR analysis

The external tools must be run outside R; IsoformSwitchAnalyzeR provides FASTA outputs and re-imports the parsed results. Plan for ~30-60 minutes of external compute on typical mammalian transcriptomes.

NMD Prediction (The 50-nt Rule)

A transcript is predicted NMD-sensitive if its premature termination codon (PTC) lies >50-55 nt upstream of the last exon-exon junction (Maquat 2004 Nat Rev Mol Cell Biol; Lykke-Andersen & Jensen 2015 Nat Rev Mol Cell Biol).

Mechanism: Spliceosome deposits the Exon Junction Complex (EJC) ~20-24 nt upstream of every exon-exon junction. During the pioneer round of translation, ribosome reading through removes EJCs upstream of the stop codon. If a stop codon precedes the last EJC by >50 nt, the EJC remains, recruits UPF1 -> SMG1 phosphorylation -> SMG6/SMG7 -> mRNA decay.

Caveats and exceptions:

• Last-exon PTCs escape NMD — can be dominant-negative or gain-of-function (e.g. MYH7 truncating variants).
• 3'UTR length matters: very long 3' UTRs (>1 kb past stop) trigger NMD via UPF1 binding even without EJCs (faux-3'UTR rule).
• Tissue-specific NMD: SMG6 vs SMG5/7 ratios vary; UPF1 stress conditions modulate.
• PTC distance must be measured on the spliced transcript, not the genomic distance.
• ~10-20% of "predicted NMD" transcripts escape NMD per orthogonal RNA-seq (Lindeboom 2016 Nat Genet; ~22% of canonical PTC-bearing transcripts escape in some tissues). Treat NMD prediction as probabilistic, not certain.

IsoformSwitchAnalyzeR's analyzeSwitchConsequences with 'NMD_status' evaluates this from the predicted ORF + transcript model.

AS-NMD as a Regulatory Layer

A large class of conserved alternative splicing events is deliberately PTC-introducing to titrate functional protein levels:

• All major SR proteins (SRSF1-12) autoregulate via poison exons (Lareau 2007 Nature; Ni 2007 Genes Dev)
• All major hnRNPs likewise
• ~70% of ribosomal protein genes use AS-NMD (Mauger 2016 Neuron; Pirnie 2017 RNA)
• SCN1A poison exon -> Stoke STK-001 ASO in Phase 1/2 for Dravet syndrome (Han 2020 Sci Transl Med)

Functional implication: an increase in PSI of a poison exon decreases functional protein. Sign-of-effect in DTU output is opposite from intuition for these genes. Always check whether the alternative form is PTC-bearing before interpreting direction.

Disease examples:

• TDP-43 cryptic exons (UNC13A, STMN2) introduce PTCs -> NMD on disease-relevant transcript (Brown 2022 Nature)
• Last-exon variants in MYH7, CARDIA: escape NMD -> dominant-negative protein

Manual DTU Pipeline (DRIMSeq + DEXSeq + stageR)

The canonical reference is the F1000Research "Swimming downstream" workflow (Love, Soneson, Patro 2018; Bioconductor rnaseqDTU).

library(tximeta); library(DRIMSeq); library(DEXSeq); library(stageR)

se <- tximeta(coldata)
counts <- assays(se)$counts

samples <- data.frame(
    sample_id = colnames(counts),
    condition = c('control', 'control', 'control', 'treatment', 'treatment', 'treatment')
)

txdf <- data.frame(
    gene_id = rowData(se)$gene_id,
    feature_id = rowData(se)$tx_id,
    counts
)

d <- dmDSdata(counts = txdf, samples = samples
d  dmFilterd min_samps_feature_expr   min_feature_expr  
              min_samps_feature_prop   min_feature_prop  
              min_samps_gene_expr   min_gene_expr  

design_full  model.matrix condition data  samplesd

dxd  DEXSeqDataSet
    countData  as.matrixcountsd  
    sampleData  samplesd
    design   sample  exon  conditionexon
    featureID  countsdfeature_id
    groupID  countsdgene_id

dxd  estimateSizeFactorsdxd
dxd  estimateDispersionsdxd quiet  
dxd  testForDEUdxd reducedModel   sample  exon
qval  perGeneQValueDEXSeqResultsdxd

dxr  DEXSeqResultsdxd independentFiltering  
pConfirmation  matrixdxrpvalue ncol  
rownamespConfirmation  dxrfeatureID
tx2gene  as.data.framedxr  

stageRObj  stageRTx
    pScreen  qval
    pConfirmation  pConfirmation
    pScreenAdjusted  
    tx2gene  tx2gene

stageRObj  stageWiseAdjustmentstageRObj method   alpha  

results  getAdjustedPValuesstageRObj order   onlySignificantGenes  

stageR semantics:

• Stage 1 (screening): gene-level p-value (perGeneQValue from DEXSeq, or DRIMSeq's gene-level p) is filtered at the desired Overall FDR.
• Stage 2 (confirmation): only within significant genes, individual transcripts are tested at a within-gene FWER computed to maintain global OFDR.
• Net effect: gene-level FDR is properly controlled, AND the transcript that drove the call is known.
• Without stageR: naive transcript-level BH overcounts because the gene-level multiple-testing burden is ignored.

fishpond/swish for Inferential-Uncertainty-Aware Testing

Goal: Test DTE while propagating quantification uncertainty from Salmon's Gibbs samples.

Approach: Run Salmon with --numGibbsSamples 20, import with tximeta, then use swish to average a non-parametric SAMseq-style test across inferential replicates.

library(fishpond); library(tximeta)

se <- tximeta(coldata)
y <- scaleInfReps(se)
y <- labelKeep(y)
y <- y[mcols(y)$keep, ]

set.seed(1)
y <- swish(y, x = 'condition')

dte_results <- as.data.frame(mcols(y))
sig <- subset(dte_results, qvalue < 0.05)

infRV (inferential relative variance) is a per-feature uncertainty diagnostic; high-infRV transcripts are unreliable and can be filtered before testing. Critical for genes with many similar isoforms (TTN, MAPT, NEFM) where Salmon's EM is uncertain.

Per-Tool Failure Modes

DEXSeq: Slowness at Scale

Trigger: Bulk cohort with >50 samples or single-cell DTU.

Mechanism: DEXSeq fits a NB GLM per exon-bin per gene; computational cost scales linearly with samples × bins.

Symptom: estimateDispersions takes hours; testForDEU exhausts memory.

Fix: Switch to satuRn (designed for scale, including scRNA-seq); run with parallelization (BPPARAM = MulticoreParam(8)).

DRIMSeq: Filtering Sensitivity

Trigger: Default dmFilter parameters too strict for low-expression cohort.

Mechanism: min_samps_feature_expr = 3, min_feature_expr = 10 drops transcripts seen in <=2 samples or with <10 counts.

Symptom: Most candidate genes filtered out; few testable genes.

Fix: Tune to dataset: lower thresholds for low-coverage data, raise for high-coverage. Document choice.

satuRn: Empirical-Bayes Shrinkage Limits

Trigger: Very small cohort (n=2 vs n=2) or very heterogeneous.

Mechanism: Empirical-Bayes shrinkage assumes shared dispersion across genes; collapses with too-few or too-heterogeneous samples.

Symptom: Inflated p-values; few discoveries despite real effects.

Fix: Aggregate replicates (pseudobulk), or switch to DEXSeq for small cohorts; use larger cohorts when possible.

swish: Salmon Gibbs Requirements

Trigger: Running swish on Salmon output without Gibbs samples.

Mechanism: swish averages over inferential replicates from Salmon's Gibbs sampler; requires --numGibbsSamples 20 (or bootstrap with --numBootstraps) at Salmon time.

Symptom: scaleInfReps errors about missing inferential replicates.

Fix: Re-run Salmon with --numGibbsSamples 20; this triples Salmon runtime but enables uncertainty-aware testing.

IsoformSwitchAnalyzeR: External-Annotator Failure

Trigger: Forgetting to run all 4 external annotators (CPC2, Pfam, SignalP, IUPred2A).

Mechanism: analyzeSwitchConsequences silently drops consequence types for which annotation wasn't imported.

Symptom: extractConsequenceSummary shows fewer types than requested; specific consequence reports missing.

Fix: Verify all 4 result files exist before analyzeSwitchConsequences; check aSwitchList$AlternativeSplicingAnalysis slot for completeness.

Reconciliation: When DTU and Event-Level Disagree

Pattern	Likely cause	Action
Significant DTU, no rMATS hit	DTU shift across many transcripts; no single canonical event captures it	Examine isoform structure in switchPlot; report at gene level
rMATS sig, no significant DTU	Single event in single isoform; not a gene-level DTU	Report as event-level result; DTU not the right framing
Both sig, same gene, different "main" isoforms	Annotation differs (rMATS uses GENCODE basic; ISA uses comprehensive)	Standardize annotation; re-run
DTU shows poison-exon switch, gene-level DGE shows decrease	NMD-coupled regulation: AS-NMD reducing protein on top of transcription	Mechanism: AS-NMD; report direction carefully

For high-confidence reporting: concordant DTU + event-level + sashimi visualization.

Single-Cell DTU

For scRNA-seq, satuRn scales where DEXSeq does not. IsoformSwitchAnalyzeR v2 supports single-cell input via importRdata with single-cell count matrices, and the underlying satuRn test has explicit single-cell calibration (Gilis 2022 F1000Research).

Strong recommendation: pseudobulk by cell type first; per-cell DTU is rarely powered with droplet 3' chemistry. See single-cell-splicing for chemistry-specific limitations.

Visualization

extractTopSwitches(
    aSwitchList,
    filterForConsequences = TRUE,
    n = 25,
    sortByQvals = TRUE
)

switchPlot(
    aSwitchList,
    gene = 'TARGET_GENE',
    condition1 = 'control',
    condition2 = 'treatment',
    localTheme = theme_bw(base_size = 12)
)

extractConsequenceSummary(aSwitchList, consequencesToAnalyze = 'all', plotGenes = FALSE)
extractConsequenceEnrichment(aSwitchList, consequencesToAnalyze = 'all')
extractSplicingSummary(aSwitchList, asFractionTotal = FALSE)

Significance Thresholds

Parameter	Default	Notes
isoform_switch_q_value	< 0.05	Switch significance
dIF (delta isoform fraction)	> 0.1	Minimum biological effect
Consequence q-value	< 0.05	Significance per consequence type
Gene-level OFDR (stageR)	< 0.05	Gene-level screening FDR
satuRn alpha	0.05	Empirical-Bayes alpha
swish qvalue	< 0.05	Local FDR from qvalue package

Common Errors

Error	Cause	Solution
Error in importRdata: ... transcript_ids do not match	Salmon index built from different annotation than provided GTF	Rebuild Salmon index with matching transcripts.fa
analyzeSwitchConsequences: not enough switching genes	preFilter too strict; few candidate switches	Lower geneExpressionCutoff, dIFcutoff in test step
dmFilter: empty result	Filter parameters too strict	Reduce min_feature_expr, min_samps_feature_expr
satuRn: rank-deficient design matrix	Confounder perfectly correlated with condition	Drop the confounder or stratify analysis
swish: no inferential replicates found	Salmon run without --numGibbsSamples	Re-run Salmon with --numGibbsSamples 20
analyzeIUPred2A: file not found	External annotator output missing or wrong path	Verify CPC2/Pfam/SignalP/IUPred2A all completed and paths match

Common Pitfalls

• Skipping stageR -> inflated transcript-level FDR; gene-level multiple-testing burden ignored.
• Forgetting NMD direction -> sign-of-effect on protein opposite to sign-of-effect on transcript when alternative form is a PTC-bearer. Always check.
• Treating short-read-derived isoform calls as ground truth -> Salmon EM is uncertain; use Gibbs samples + swish if quantification uncertainty matters.
• Comparing across annotations -> GENCODE basic vs comprehensive, RefSeq, Ensembl all have different transcript catalogs; switches "appear" or "disappear" with annotation choice. Document version.
• Not running long-read where possible -> Iso-Seq / ONT removes ambiguity for genes with many similar isoforms (TTN, MAPT, NEFM, DSCAM).
• Choosing satuRn or DEXSeq blindly at the n=5 boundary -> IsoformSwitchAnalyzeR v2 auto-selects based on >5 vs <=5; results may differ. Document choice.
• Reporting a "switch" without a sashimi plot -> reviewers will demand it; do it upfront.
• Forgetting stageR also corrects gene-level p when starting from DRIMSeq -> DRIMSeq's gene_p should be passed as pScreen, not raw transcript p-values.

Related Skills

• differential-splicing - Event-level (rMATS, leafcutter, MAJIQ) complementary to DTU
• splicing-quantification - PSI is a 1D projection of DTU shifts
• splicing-qc - Verify upstream library, depth, alignment before DTU
• sashimi-plots - Required visualization for switch validation and reporting
• splice-variant-prediction - Connects SpliceAI variant predictions to specific isoforms
• long-read-splicing - Full-isoform DTU bypasses transcript-quant uncertainty; preferred for many-isoform genes
• pathway-analysis/go-enrichment - Pathway enrichment of switching genes
• rna-quantification/alignment-free-quant - Salmon with --numGibbsSamples is upstream

References

• Vitting-Seerup 2025 bioRxiv - IsoformSwitchAnalyzeR v2
• Vitting-Seerup & Sandelin 2017 Bioinformatics - IsoformSwitchAnalyzeR original
• Anders et al 2012 Genome Res - DEXSeq
• Nowicka & Robinson 2016 F1000Research - DRIMSeq
• Gilis et al 2022 F1000Research - satuRn
• Zhu et al 2019 NAR - swish / fishpond
• Van den Berge et al 2017 Genome Biol - stageR
• Love, Soneson, Patro 2018 F1000Research - Swimming downstream DTU workflow
• Maquat 2004 Nat Rev Mol Cell Biol - NMD review
• Lykke-Andersen & Jensen 2015 Nat Rev Mol Cell Biol - NMD update
• Lindeboom et al 2016 Nat Genet - NMD escape rates from RNA-seq
• Lareau et al 2007 Nature - SR protein AS-NMD autoregulation
• Mauger et al 2016 Neuron - ribosomal protein AS-NMD
• Brown et al 2022 Nature - UNC13A cryptic exon (TDP-43)
• Han et al 2020 Sci Transl Med - SCN1A poison exon ASO