How are protein-protein interaction networks constructed and analyzed?

Protein-protein interaction (PPI) networks represent physical or functional relationships between proteins. Construction sources: 1) Experimental - yeast two-hybrid, co-immunoprecipitation, affinity purification mass spectrometry (AP-MS). 2) Databases - STRING, BioGRID, IntAct compile curated interactions. 3) Computational prediction - gene co-expression, domain interactions, phylogenetic profiles. Analysis methods: 1) Network topology - identify hubs (highly connected nodes), betweenness centrality (information flow). 2) Clustering - detect protein complexes and functional modules using MCL, MCODE. 3) Enrichment analysis - determine pathway/GO enrichment of clusters. 4) Integration - overlay with expression data, mutations. Tools: Cytoscape for visualization, NetworkX/igraph for analysis.