Pathway Enrichment & Topology-Based Analytics — Hands-on

Learn how to move beyond plain gene lists and connect omics results to pathways and networks using enrichment and topology based analytics. This module covers over representation analysis, GSEA style rank based methods, and network topology aware scores that highlight key pathways, nodes and modules driving phenotypes.

Pathway Enrichment & Topology-Based Analytics

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Session Index

Session 1 — Pathway Enrichment Foundations Session 2 — GSEA, Rank & Sample Level Methods Session 3 — Topology Based & Network Aware Analytics Session 4 — Mini Capstone: Pathway Enrichment Report

Session 1

Fee: Rs 8800

Pathway Enrichment Foundations

From gene lists to pathway level insights

when to use enrichment background universe choice multiple testing concepts

Over representation analysis (ORA) basics

hypergeometric and Fisher tests p values, FDR and ranking interpretation and caveats

Toolchain for basic enrichment analysis

R based enrichment packages Python based wrappers web tools overview (concept only)

Session 2

Fee: Rs 11800

GSEA, Rank & Sample Level Methods

Gene set enrichment analysis (GSEA) concepts

ranked lists and enrichment scores permutation strategies leading edge subsets

Single sample and variation based methods (concepts)

GSVA style approaches ssGSEA like profiles pathway scores per sample

Implementation toolkit for GSEA style workflows

R based GSEA implementations ranked statistics preparation plots for enrichment curves

Session 3

Fee: Rs 14800

Topology Based & Network Aware Analytics

Why topology matters in pathway analysis

beyond simple membership counts edge structure and direction central and peripheral nodes

Topology based impact and perturbation scores (concepts)

node and edge centrality ideas shortest path and flow thinking downstream impact style metrics

Implementation toolkit for topology aware analysis

network packages in R and Python Cytoscape network metrics visualisation of key nodes and paths

Session 4

Fee: Rs 18800

Mini Capstone: Pathway Enrichment Report

Perform end to end enrichment and topology analysis on a dataset

Theory + Practical

Summarise key pathways, hubs and modules driving the phenotype

ranked pathway tables enrichment plots and maps network style figures

Deliverables: notebook, enrichment tables & visual report

R or Python notebook CSV/TSV enrichment outputs PDF/HTML pathway summary

PDF

Pathway Enrichment & Topology-Based Analytics Training | GSEA, ORA & Network-Aware Scores

Pathway Enrichment & Topology-Based Analytics — Hands-on