Networks represent the interactions among components of biological systems. In the context of high dimensional omics data, relevant networks include gene regulatory networks, protein-protein interaction networks, and metabolic networks.
These networks provide a window into biological systems as well as complex diseases, and can be used to understand how biological functions are implemented and how homeostasis is maintained. On the other hand, pathway-based analyses can be used to leverage biological knowledge available from literature, gene ontologies or previous experiments in order to identify the pathways associated with disease or an outcome of interest.
In this module, various statistical learning methods for reconstruction and analysis of networks from omics data are discussed, as well as methods of pathway enrichment analysis. Particular attention is paid to omics datasets with a large number of variables, e.g. genes, and a small number of samples, e.g. patients.
The techniques discussed will be demonstrated in R. This course assumes familiarity with R or other command-line programming languages.