Table 1 Analysis of the overlap of the cured genes with GO: biological processes and cellular components annotated sets in MsigDB
Gene Set Name | Description | Genes in the overlap (number, genes) | p-value | FDR q-value |
|---|---|---|---|---|
Side of membrane | A cellular component consisting of one leaflet of a membrane bilayer and any proteins embedded or anchored in it or attached to its surface. | 19: HLA-DRB1, HLA-DRB3, HLA-DRB4, HLA-DRB5, HLA-DQB1, CTLA-4, CD3E, TRBC1, CD59, IL2RA, CD27, ICOS, CD2, KLRD1, ITGA6, IL2RB, KCNJ5, TNFRSF9, SERPINE2 | 5.17e−16 | 4.44e−12 |
External side of plasma membrane | The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface. | 15: HLA-DRB1, CTLA-4, CD3E, TRBC1, CD59, IL2RA, CD27, ICOS, CD2, KLRD1, ITGA6, IL2RB, KCNJ5, TNFRSF9, SERPINE2 | 6.50e−14 | 2.78e−10 |
T cell receptor signaling pathway | A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell. | 11: HLA-DRB1, CTLA-4, CD3E, TRBC1, HLA-DRB3, HLA-DRB4, HLA-DRB5, HLA-DQB1, GATA3, TRAC, EIF2B2 | 3.05e−12 | 8.72e−09 |
Cell surface | The external part of the cell wall and/or plasma membrane. | 18: HLA-DRB1, CTLA-4, CD3E, TRBC1, CD59, IL2RA, CD27, ICOS, CD2, KLRD1, ITGA6, IL2RB, KCNJ5, TNFRSF9, SERPINE2, TIGIT, PTPRK, MMP7 | 5.10e−12 | 1.09e−08 |
Positive regulation of immune system process | Any process that activates or increases the frequency, rate, or extent of an immune system process. | 19: HLA-DRB1, CTLA-4, CD3E, TRBC1, CD59, IL2RA, CD27, ICOS, CD2, HLA-DRB3, HLA-DRB4, HLA-DRB5, HLA-DQB1, GATA3, TRAC, EIF2B2, PRKCE, ETS1, KLF10 | 1.43e−11 | 2.45e−08 |
Regulation of immune system process | Any process that modulates the frequency, rate, or extent of an immune system process. | 22: HLA-DRB1, CTLA-4, CD3E, TRBC1, CD59, IL2RA, CD27, ICOS, CD2, KLRD1, HLA-DRB3, HLA-DRB4, HLA-DRB5, HLA-DQB1, GATA3, TRAC, EIF2B2, TIGIT, PRKCE, ETS1, KLF10, KLRB1 | 3.57e−11 | 5.10e−08 |
MHC class II protein complex | A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen. | 5: HLA-DRB1, HLA-DRB3, HLA-DRB4, HLA-DRB5, HLA-DQB1 | 3.04e−10 | 3.43e−07 |
Antigen receptor mediated signaling pathway | A series of molecular signals initiated by the cross-linking of an antigen receptor on a B or T cell. | 11: HLA-DRB1, CTLA-4, CD3E, TRBC1, HLA-DRB3, HLA-DRB4, HLA-DRB5, HLA-DQB1, GATA3, TRAC, EIF2B2 | 3.20e−10 | 3.43e−07 |
Intrinsic component of plasma membrane | The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane. | 21: HLA-DRB1, CTLA-4, CD3E, CD59, IL2RA, CD27, ICOS, CD2, ITGA6, IL2RB, KCNJ5, TNFRSF9, HLA-DRB3, PTPRK, ADCY3, ELAPOR1, GABRB1, TSPAN5, SLC12A6, LRP12, P2RY10 | 6.85e−10 | 6.53e−07 |
Activation of immune response | Any process that initiates an immune response. | 13: HLA-DRB1, CTLA-4, CD3E, TRBC1, CD59, HLA-DRB3, HLA-DRB4, HLA-DRB5, HLA-DQB1, GATA3, TRAC, EIF2B2, PRKCE | 9.68e−10 | 8.30e−07 |