Traditional Analysis
•After searching all information about these 100 genes, it is still difficult to know which biological processes are most significantly altered
50
Gene 1
Apoptosis
Cell-cell signaling
Protein phosphorylation
Mitosis
…
Gene 2
Growth control
Mitosis
Oncogenesis
Protein phosphorylation
…
Gene 3
Growth control
Mitosis
Oncogenesis
Protein phosphorylation
…
Gene 4
Nervous system
Pregnancy
Oncogenesis
Mitosis
…
Gene 100
Positive ctrl. of cell prolif
Mitosis
Oncogenesis
Glucose transport
…
Adopted from http://www.geneontology.org/
Typically, this is the way the analysis would have been done.

Taking your differentially regualted genes, you’d analyse them one by one - researching the what is known about that gene, and what processes it is involved in.