Objectives

  1. Review top level goals of functional analysis
  2. Review remianing topics for the workshop.
  3. Walk through FCS/GSEA’s approach to functional analysis.

Common functional analysis approaches

  • ORA
  • FCS / GSEA
  • TP

Similar steps / Similar inputs / Similar outputs Our focus / path in this workshop

ORA Review

Schematic

ORA Pros

  • Analysis is relatively simple to execute.
  • Interpretation is straightforward.
  • Supports a wide range of biological processes and model systems.
  • Significant results are a robust indicator of biological activity.

ORA Cons

  • Requires a background set of genes. Generally straightforward for RNA-Seq (transcriptome) or microarray, more nuanced for proteins.

  • Requires a subset of diffex genes, usually partitioned with arbitrary cutoff value. Too few diffex genes or too many diffex genes will miss real functional relationships.

  • Treats all genes the same; doesn’t care whether the gene is over or under or by how much. (That’s why the inputs are not ranked or ordered - they are simply sets of genes.)

FCS/GSEA

An example sc RNA-Seq experiment.