Table 2.
Gene set enrichment analysis results comparing the ABCD clone to the EF clone
| Gene ontology | P-value | FDR |
|---|---|---|
| MHC protein complex | 4.85e-15 | 1.32e-11 |
| Antigen processing and presentation of endogenous antigen | 6.40e-15 | 1.32e-11 |
| MHC class I protein complex | 6.57e-14 | 8.08e-11 |
| Response to type I interferon | 2.86e-11 | 1.60e-08 |
| Antigen processing and presentation of endogenous peptide antigen | 2.61e-10 | 1.14e-07 |
| Positive regulation of T cell mediated cytotoxicity | 7.96e-09 | 2.51e-06 |
| Interferon Gamma mediated signaling pathway | 2.08e-08 | 5.72e-06 |
| Regulation of T cell mediated cytotoxicity | 2.37e-08 | 6.07e-06 |
| Positive regulation of antigen processing and presentation | 4.99e-07 | 9.59e-05 |
| Detection of other organism | 6.87e-07 | 1.28e-04 |
Top 10 most significantly down regulated pathways are shown (first column) along with p-value (middle column) and false discovery rates (third column). The Correlation Adjusted MEan RAnk gene set test is used, which performs a 2-sided test and uses Benjamini–Hochberg algorithm to produce false discovery rate (FDR) accounting for multiple comparisons38.