From: Exploring pathway interactions to detect molecular mechanisms of disease: 22q11.2 deletion syndrome
 | Pathway Interaction | Pathway ORA |
---|---|---|
Database Used | WikiPathways, STRING | WikiPathways |
Detected Unit | Significant path (two or more genes connected by protein-protein interaction) | Individual gene |
Selection Criteria | Sum of weights (transformed T-statistics) | P-value and log2FC score |
Resulting Subnetwork | Pathway-gene-gene-pathway | Gene-pathway-gene-pathway |
Biological Processes Identified for Psychiatric 22q11DS | NK cell function PI3K/Akt signalling | NK cell function PI3K/Akt signalling |
Strength | Can detect multiple genes collectively having a strong expression profile, backed by prior knowledge. | Can detect single strongly expressed genes using flexible criteria. |
Weakness | Strongly dependent on pre-existing relationships between gene products. Genes with unidentified relationships will be ignored. Detection criteria are hard to adjust or modify. | Individual gene selection can be highly dependent on the significance criteria. Depending on data quality, spurious genes might be mistaken as being significant. |