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