Protein–Protein Interaction Networks & Cluster Analysis — Hands-on

Learn how to construct, curate, and mine protein protein interaction (PPI) networks for biological insight. This module covers PPI databases and evidence scores, network assembly and filtering, cluster and module detection, and functional interpretation using enrichment and disease gene overlays in Cytoscape and Python/R.

Protein–Protein Interaction Networks & Cluster Analysis

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Session Index

Session 1 — PPI Databases & Evidence Sources Session 2 — Network Assembly & Filtering Session 3 — Cluster Detection & Module Interpretation Session 4 — Mini Capstone: PPI Module & Enrichment

Session 1

Fee: Rs 8800

PPI Databases & Evidence Sources

Overview of protein protein interaction resources

STRING BioGRID IntAct / DIP

Interaction types and evidence channels

experimental evidence database curated text mining and prediction

Toolchain for PPI data retrieval

API queries and bulk downloads identifier mapping (UniProt) tabular PPI formats (TSV)

Session 2

Fee: Rs 11800

Network Assembly & Filtering

Building PPI networks from interaction tables

source and target mapping unweighted vs weighted edges directed vs undirected views

Quality control and evidence based filtering

score thresholds interaction type filters removing low support edges

Implementation toolkit for PPI graphs

Python / networkx R / igraph Cytoscape import and layout

Session 3

Fee: Rs 14800

Cluster Detection & Module Interpretation

Detecting densely connected PPI clusters

MCODE Markov clustering (MCL) Louvain style community detection

From clusters to functional modules

GO enrichment per cluster pathway enrichment (KEGG, Reactome) disease gene overlays

Visual analytics and reporting of modules

Cytoscape styles and layouts module level summary tables export ready figures

Session 4

Fee: Rs 18800

Mini Capstone: PPI Module & Enrichment

Build and analyse a disease or pathway specific PPI network

Theory + Practical

Identify key clusters and interpret biological roles

hub and bottleneck proteins module enrichment results candidate targets or biomarkers

Deliverables: notebook, network files & report

Python/R notebook SIF / GraphML / CSV PDF/HTML module summary

PDF

Protein–Protein Interaction Networks & Cluster Analysis Training | PPI Databases, Clusters, Modules

Protein–Protein Interaction Networks & Cluster Analysis — Hands-on