How are Gene Set Enrichement Analysis and Sub-Network Enrichement Analysis calculated?
Sub-Network Enrichment Analysis (SNEA)
The following steps describe the computational steps performed in SNEA.
1.) Preparation of Sub-Networks
SNEA builds Sub-networks from the relationships in a database based on the criterion specified by user. It starts by creating a central "seed" from all relevant entities in the database, and retrieving associated entities based on their relationship with the seed (i.e. binding partners, expression targets, protein modification targets, etc).
2.) Calculation of Background Distribution
The algorithm calculates a background distribution of all expression values for the selected sample in the experiment, typically from a differential measurement such as resulting from "Find Differentially Expressed Genes" tool.
3.) Calculation of Sub-Network Distribution
"sub-network" distribution of the expression values is then calculated in a similar manner for all sub-networks constructed in the previous step. Importantly, during distribution calculation, the expression value for each entity connected to a seed is accounted for as many times as the connectivity of that entity in ResNet. The purpose of this correction is to correct the bias introduced by different connectivities of entities in ResNet.
4.) Statistical Comparison of Sub-Network Distribution with Background Distribution
The algorithm compares the sub-network distribution to the background distribution using one-sided Mann-Whitney U-Test, and calculates a p-value indicating the statistical significance of difference between two distributions.
5.) Presentation and Prioritization of Results
Pathway Studio Explore presents the "seed" entity for each sub-network along with the sub-networks themselves in the user interface, ranked from lowest (best) to highest (worst) p-Value.
Gene Set Enrichment Analysis (GSEA)
The Gene Set Enrichment Analysis proceeds identically to the Sub-Network Enrichment Analysis with the following exceptions:
Step 1: Sub-networks are not prepared on the fly. Rather the algorithm considers pathways and groups which were previously created by the end-user, imported into Pathway Studio, or provided in the ResNet Database by Ariadne.
Step 5: Statistical comparison is done using the Mann-Whitney test (described above) or Kolmogorov-Smirnov statistical algorithms.
