Responder & Non-Responder Analysis
Identify what separates responders from non-responders in Phase 1/2 trial biopsy cohorts, with confounding-adjusted causal inference, multi-layer mechanism recovery, and directionality-aware translational shortlists in a single workflow.
Deliverables
Confounding-adjusted responder signature with multi-layer escalation
Multi-method differential expression (limma, DESeq2) with covariate adjustment for trial-design confounders (severity, therapy arm, batch, site). Inverse-probability-of-treatment-weighting and doubly-robust AIPW sensitivity. E-value sensitivity to unmeasured confounding. When single-gene FDR is bound by structural confounding, as it was in PROTECT (severity-therapy collinearity χ²=139.88, zero genes at FDR<0.05 post-adjustment), Inflexa automatically escalates to pathway, TF, network, and immune-deconvolution layers and recovers the signal there.
Convergent mechanism architecture
Coherent transcriptional programmes recovered from GSEA pathway enrichment, decoupleR TF activity (CollecTRI), WGCNA module hubs, and immune deconvolution, with concordance checked across layers. Programmes get a literature-grounded narrative assembled from PubMed: Inflexa runs targeted PubMed queries against each programme's hub genes, transcription factors, and enriched pathways, traces the evidence chains, and inlines source citations into the dossier. In PROTECT this surfaces as a two-programme architecture: loss of colonocyte identity (Programme A, anchored by SLC26A3, CDX2, HNF1A, FXR) and active inflammatory signalling (Programme B, RELA / STAT3 / NFKB1 / HIF1A drive, CXCL13 lead).
Directionality-aware tractability triage
For every prioritised candidate, restoration-vs-inhibition direction is computed, then matched against existing chemistry inventories. Counter-mechanistic disqualifications surface before safety review. In PROTECT, FGFR3 inhibitors and pan-CA inhibitors are both counter-mechanistic; FGFR3 is doubly disqualified for pediatric use on growth-plate biology. Multi-mechanism convergence raises priors for restoration targets when independent chemistries hit the same axis: the PPARγ → CDX2 → SLC26A3 axis is hit by rosiglitazone, sodium butyrate, dexamethasone, and FXR agonism.
Move from a confounded responder cohort to a defensible biomarker, MoA, and tractability shortlist your translational team can act on: restoration targets pursued with the right chemistry, counter-mechanistic disqualifications removed up front, mechanism evidence chains traced to PubMed source for internal review.
PROTECT pediatric UC re-analysis: confounding, programmes, and tractability
5-ASA was prescribed exclusively to Low-severity patients. CS-IV concentrated in High-severity disease. Single-gene signal is structurally bounded; the agent escalates.
Only 4 genes reach E ≥ 3, the threshold for ROBUST_STRONG. When the single-gene signal is confounding-bound, the platform escalates to pathway, TF, and network layers.
Pathway-level signal survives confounding adjustment. Coherent programmes emerge from convergent layers.
Two-programme architecture: colonocyte-identity restoration drivers (CDX2, CDX1, HNF1A, FXR) above zero; inflammatory-signalling drivers (RELA, STAT3, NFKB1, HIF1A) below.
| Candidate | Direction | Tier | Note |
|---|---|---|---|
| FGFR3 | Restoration | T1 | Counter-mechanistic: inhibitors disqualified |
| SLC26A3 | Restoration | T2 | Inhibitor-only chemistry; needs activator series |
| CDX2 | Restoration | T5 | Restored via PPARγ → CDX2 axis (rosiglitazone, butyrate) |
| CXCL13 | Inhibition | T4 | Biologic only; no clinical-stage agent in IBD |
| RELA | Inhibition | T5 | Programme B driver; hit by JAK1 inhibition (upadacitinib) |
PROTECT is one example. The full case study traces the confounding adjustment, the two-programme architecture, the directionality framework that disqualifies FGFR3 inhibitors entirely, and the pediatric translational re-ranking that surfaces sodium butyrate, upadacitinib, and anti-CXCL13 as the three actionable programmes. Read the full PROTECT case study → /news/protect-pediatric-uc-responder-analysis
Methodology
Cohort design assessment + confounding triage
Inflexa inventories design covariates (severity, therapy arm, batch, site, demographics), runs the contingency tests, and flags structural confounding before analysis. In PROTECT this immediately surfaced χ²=139.88 between therapy and severity, bounding what single-gene analysis could discover.
Multi-method DE with sensitivity
limma and DESeq2 with covariate adjustment for the flagged confounders. Inverse-probability-of-treatment-weighting and doubly-robust AIPW sensitivity. E-value computation per gene against unmeasured confounders, returning a genome-wide robustness profile.
Multi-layer enrichment escalation
GSEA against Hallmark, Reactome, and custom collections; decoupleR TF activity (CollecTRI ULM); WGCNA modules with eigengene-trait correlation; immune deconvolution. Cross-layer concordance check identifies the coherent programmes that survive when single-gene signal does not.
PubMed-curated MoA narrative
For each programme, Inflexa runs targeted PubMed queries against the programme's hub genes, transcription factors, and enriched pathways. Literature evidence chains are assembled (basic → preclinical → clinical) and inlined into the dossier with full provenance to PMID.
Tractability triage with directionality + dossier assembly
Direction-of-effect per candidate; tractability tiering against ChEMBL and DrugBank inventories; multi-mechanism convergence layered on; directionality-mismatched candidates flagged. Full dossier assembled with provenance, ready for translational, clinical, and external review.
Target personas
Translational medicine lead
Build a defensible responder/non-responder story from a Phase 1/2 cohort, with convergent mechanism evidence and a tractability-triaged shortlist your discovery and safety teams can act on.
Exploratory biomarker scientist
Recover a coherent biomarker signature when single-gene FDR is bound by trial-design confounding. Multi-layer escalation and convergent evidence stacks beat bigger gene lists.
Clinical pharmacologist
Couple responder transcriptomics to mechanism and direction-of-effect, so candidate triage reflects what restoration-vs-inhibition pharmacology can actually achieve in patients.
Explore more
Bring us a Phase 1/2 cohort.
Tell us about a translational dataset you care about. We'll scope a paid discovery collaboration in 2–3 weeks and run a full analysis with weekly check-ins.