Functional Enrichment Studio

BioInfo Tools

Functional Enrichment Studio app: upload annotations table + a gene list, pick a factor (KO, Pathway, COG, PFAM, GO, EC, Module, Reaction, BRITE, rclass, TC, CAZy, BiGG), hit Run, and explore analysis results via table or charts.

Main page: https://hugston.com/bioinfo

BioInfo_github_1.mp4

Features

Hugston analysis everything runs in the browser.

• Flexible inputs: CSV / TSV / TAB / TXT / XLS / XLSX.
• Smart column detection: guesses #query / query / New_locus_tag, and factor columns like KEGG_ko, KEGG_Pathway, PFAMs, GOs, etc.
• Multiple term families: KO, Pathway, COG, PFAM, GO, EC, Module, Reaction, BRITE, rclass, TC, CAZy, BiGG.
• Proper stats: right-tail hypergeometric; BH/BY FDR.
• Rich visuals: Bar, Volcano, Sunburst, Manhattan, Heatmap, Sankey, Overview grid; interactive clicks deep-link to KEGG/GO/InterPro/etc.
• Exports: CSV/JSON for results, PNG for charts.
• Demo: “Load Demo” button seeds tiny test data and auto-runs.

---

Functional Enrichment Studio: How to Use

1. Upload files

   • Annotations: eggNOG-style table with a gene ID column (#query / query / New_locus_tag) and any of:
     • KEGG_ko
     • KEGG_Pathway
     • COG_category
     • PFAMs
     • GOs
     • EC
     • KEGG_Module
     • KEGG_Reaction
     • BRITE
     • KEGG_rclass
     • KEGG_TC
     • CAZy
     • BiGG_Reaction
   • Gene list: one ID per line or a 1-column sheet (header optional).

2. Pick settings

   • Factor (e.g., KO or Pathway)
   • Background set
   • Multi-hit handling
   • FDR method/cutoff

3. Run
   Results render in the Table tab; charts appear in other tabs.

---

Interact

• Click table rows to inspect in-list vs background genes.
• Click chart points to open external pages:
  • KEGG KO → DBGET (ko:Kxxxxx)
  • KEGG Pathway → map pages (mapxxxxx)
  • GO → AmiGO (GO:nnnnnnn)
  • PFAM → InterPro
  • EC → Expasy
  • BRITE / rclass / TC / CAZy / BiGG → respective portals

---

Export

• Results: CSV / JSON
• Charts: PNG (active chart)

---

Input Quirks It Handles

• Delimiter auto-detect: tab, comma, semicolon, pipe.
• Normalizes KOs: ko:K00001 → K00001.
• Sanitizes pathway tokens: map00010, ko00010 → usable forms.

---

Under the Hood (Stats)

Test: Right-tail hypergeometric P[X ≥ k] with:

• N = background size
• M = term count in background
• n = list size
• k = overlap

Multiple testing: BH (default) or BY FDR.

Extras:

• Odds ratio + 95% CI (Haldane–Anscombe 0.5 continuity)
• Specificity
• Information content
• Simple “escore” to rank terms for charts

---

Privacy, Performance & CDNs

• No data leaves the browser: All parsing and stats run client-side.
• External libraries: Load via CDN by default (Plotly, jStat, PapaParse, XLSX, Cytoscape).
  Switch to local bundles if your environment blocks CDNs.

---

License

This project is Hugston-licensed. See LICENSE in Hugston.com.
© 2025 Hugston. All rights reserved.

---

Acknowledgements

© 2025 Hugston
Klaudi Bregu https://github.com/Mainframework