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Report Sections
Generated by Inflexa · Feb 21, 2026
Differential Expression
Ancestry-stratified gene expression
Your analysis is done. Now present it.
After running differential expression, pathway enrichment, immune profiling, and survival analysis, you're sitting on results from multiple runs. One message turns them into a structured report.
Cortex knows what you ran. It pulls the figures, tables, and statistics from your analysis history and assembles them into presentation-ready sections.
One message. Every figure traced to its source run.
Completed Runs
I'll build a comprehensive report from your 5 analysis runs. Here's the structure:
Report Outline
Generating now: pulling figures from your DE, pathway, immune, TF, and survival runs...
Breast Cancer Ancestry Analysis: Report
13 sections · 23 figures · 8 tables · Click to open
The whole story on one screen
Every report opens with a structured summary: cohort size, total DEGs, key pathway hits, and immune signatures, all quantified and sourced to the underlying runs.
Top findings are ranked by effect size and statistical significance, not just listed. Reviewers see what matters first.
A 30-second read that replaces a 30-minute deep dive.
Study Overview
Key Findings
PI3K/Akt/mTOR pathway dominates African American tumors
SHAP importance 0.510 · NES = 2.34, FDR = 1.2e-06
Th2 immune infiltration elevated 2.3-fold in AA vs EA
Immune deconvolution · p = 4.1e-04
NT5E and estrogen response drive European ancestry classification
SHAP importance 0.234, 0.134 · Ancestry-stratified ML model
Significant survival divergence between ancestry groups
Log-rank p = 0.003 · AA 5-year OS: 72% vs EA: 84%
Every gene, in context
Interactive volcano plots render directly in the report. Hover any point to see the gene name, fold change, and adjusted p-value. Click to jump to the gene's full profile.
Cortex stratifies the analysis by ancestry group, revealing gene expression patterns that are invisible in a pooled analysis. BRCA1 shows 3.2-fold upregulation in AA samples: a signal lost when cohorts are combined.
4,217 DEGs across 3 ancestry cohorts: each plotted, searchable, and linked to downstream analyses.
Outcomes that tell the full story
Kaplan-Meier curves with confidence intervals, risk tables, and log-rank statistics, all generated from your survival run and rendered as interactive charts.
African American patients show significantly lower 5-year overall survival (72%) compared to European American (84%). The divergence becomes apparent after year 2, consistent with known ancestry-linked disparities in treatment access and tumor biology.
Clinical context that no spreadsheet can provide: survival curves stratified by your variables of interest.
Number at Risk
| Group | 0 yr | 1 yr | 2 yr | 3 yr | 4 yr | 5 yr |
|---|---|---|---|---|---|---|
| EA | 734 | 698 | 671 | 648 | 629 | 617 |
| Arab | 24 | 23 | 21 | 20 | 19 | 19 |
| AA | 326 | 302 | 278 | 258 | 242 | 235 |
Refine it like you'd brief a colleague
Reports aren't one-shot. Rearrange sections, add context, adjust visuals, all through natural language. Every edit preserves the underlying data and statistical rigor.
Tell Cortex what to change. It understands your analysis, so "add the immune comparison to the summary" doesn't require explaining what that means.
No re-running analyses. No exporting and re-importing. Just say what you want.
Before
1. Summary
2. Study Design
3. Cohort
4. DE
5. Pathways
6. Dose-Response
7. Immune
...
After
1. Summary ★
2. Study Design
3. Cohort
4. DE
5. Pathways
6. Immune
...
Before
After
Conclusions backed by every upstream analysis
The Synthesis section doesn't just summarize: it integrates. Each conclusion is linked to the specific analyses that support it, with confidence scored by evidence convergence.
When three independent analyses point to the same biological story, Cortex flags it as high-confidence. When evidence is mixed, it says so.
Not a summary of summaries. A synthesis that traces every claim to its evidence chain.
PI3K/Akt/mTOR signaling is the dominant ancestry-linked pathway in AA breast cancer
Supported by differential expression (NES=2.34), SHAP feature importance (0.510), pathway enrichment (FDR=1.2e-06), and TF activity analysis showing upstream AKT1 activation. This represents a potential therapeutic target for ancestry-stratified treatment.
Immune microenvironment composition diverges significantly by ancestry
Th2 infiltration is elevated 2.3-fold in AA tumors (p=4.1e-04). This is corroborated by LAG3 expression differences (SHAP=0.290) and survival analysis showing immune-stratified outcomes.
Estrogen receptor signaling drives EA-specific tumor biology
ESR1 and FOXA1 are top SHAP features for EA classification. Estrogen response hallmark pathway is significantly enriched in EA tumors. However, this may partly reflect subtype composition differences.
Arab cohort shows intermediate molecular profile
RA-QA cohort (n=24) clusters between EA and AA on principal components. Limited sample size precludes definitive conclusions: validation with larger Arab-ancestry datasets recommended.
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Team members or external reviewers open the link and get the full report. Every chart is interactive. Every finding is traceable. The context travels with the work.
Your collaborator sees exactly what you see, not a flattened copy.
Breast Cancer Ancestry Analysis
12 sections · 23 figures · 8 tables · Updated 2 min ago
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Shared with
Radu Tanasa
radu@panomics.bio
Sarah Chen
s.chen@research.edu
12 sections. One report. Built from your runs.
Every section generated from analysis results, not templates. Structure adapts to what you ran.
Summary
Key stats, top findings, study overview
Study Design
Cohorts, comparisons, methods used
Cohort Analysis
Sample demographics, group composition
Differential Expression
Volcano plots, DE tables, gene rankings
Pathways
Enrichment scores, pathway networks
Immune Profiling
Cell composition, infiltration estimates
TF Activity
Transcription factor regulation scores
Networks
Pathway interaction graphs
Genomics
Variant analysis, mutation profiles
Survival
KM curves, log-rank tests, risk tables
Synthesis
Integrated conclusions, confidence scores
Limitations
Caveats, power analysis, known gaps
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