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Bioinformatics lectures at Rice University
Li ZhangLecture 9: Networks and integrative genomic
analysishttp://odin.mdacc.tmc.edu/~llzhang/RiceCourse
Protein-protein interaction networks
Protein-protein interaction network in yeast.Wagner 2001.
Power law distribution
Gene duplication and divergence
P-value of association
The Method
Gene set enrichment analysis
Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes).
MSigDB Collections
C1: positional gene sets
C2: curated gene sets
C3: motif gene sets
C4: computational gene sets
C5: GO gene sets
C6: oncogenic signatures
C7: immunologic signatures
The 10295 gene sets in the Molecular Signatures Database (MSigDB) are divided into 7 major collections, and several sub collections.
Canonical pathways