Pathway Ontologies & Databases (KEGG/Reactome/BioCyc) — Hands-on

Learn how to leverage pathway ontologies and curated pathway databases to interpret omics experiments. This module walks through Gene Ontology (GO) , KEGG, Reactome, BioCyc and PathwayCommons — from manual browsing and ID mapping to scripted enrichment, topology-aware analysis and figure-ready visualization. You will implement end-to-end workflows that connect DE lists and multi-omics signatures to pathways and mechanisms.

Pathway Ontologies & Databases (KEGG/Reactome/BioCyc)

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Session Index

Session 1 — Ontologies, Pathway Resources & ID Mapping Session 2 — Pathway Enrichment & Over-Representation Analysis Session 3 — Programmatic Access, Topology & Multi-Omics Session 4 — Mini Capstone: Pathway-Centric Interpretation

Session 1

Fee: Rs 8800

Ontologies, Pathway Resources & ID Mapping

Pathway ontologies & ecosystem overview

GO BP/MF/CC KEGG / Reactome BioCyc / PathwayCommons

Identifiers, namespaces & mapping

Entrez / Ensembl / UniProt KEGG IDs / ChEBI / HMDB ID conversion pitfalls

Toolchain & portals

AmiGO / QuickGO KEGG & Reactome browsers BioCyc / PathwayCommons UI

Session 2

Fee: Rs 11800

Pathway Enrichment & Over-Representation Analysis

Classical enrichment workflows

ORA / hypergeometric tests GO/KEGG/Reactome sets multiple testing (FDR)

Rank-based & gene-set methods

GSEA / preranked GSEA GSVA & ssGSEA (overview) hallmark & custom gene sets

Tools & implementation

R: clusterProfiler / ReactomePA g:Profiler / Enrichr visual summaries & tables

Session 3

Fee: Rs 14800

Programmatic Access, Topology & Multi-Omics

APIs & programmatic interfaces

KEGGREST / bioservices Reactome API BioCyc web services

Topology-aware & network-based analyses

pathway graphs & centrality impact / topology scores link to PPI/GRN networks

Multi-omics overlays (overview)

transcriptomics + proteomics metabolomics on KEGG maps Cytoscape / PathVisio exports

Session 4

Fee: Rs 18800

Mini Capstone: Pathway-Centric Interpretation

Case study: from DE list to pathway story

Theory + Practical

Workflow & reporting

full R/Python notebook tables + enrichment plots annotated pathway diagrams

Deliverables

PDF/HTML report Rmd/Notebook + scripts requirements.txt/environment.yml

PDF

Pathway Ontologies & Databases (KEGG/Reactome/BioCyc) Training | Enrichment, Topology & APIs

Pathway Ontologies & Databases (KEGG/Reactome/BioCyc) — Hands-on