Table 1. IPA assessment of pre-defined canonical pathways affected by changes in QKI expression.
| Monocytes |
Macrophages |
||||
|---|---|---|---|---|---|
| THP-1 sh-QKI versus sh-Cont | THP-1 sh-QKI versus sh-Cont | ||||
| Affected canonical pathway | −Log (P-value) | Affected genes | Affected canonical pathway | −Log (P-value) | Affected genes |
| Atherosclerosis signalling | 9.2 | CXCL8, APOE, ICAM1, PDGFA, PLA2, G4C, CCR2, F3, LYZ, CCL2, ORM1, APOC1, IL1B, ORM2, PDGFD, TNF | Superpathway of cholesterol biosynthesis | 10.6 | FDPS, PDFT1, EBP, DHCR7, ACAT2, IDI1, HSD17B7, MSMO1, HMGCS1, CYP51A1 |
| Superpathway of cholesterol biosynthesis | 8.2 | MVD, FDPS, CHCR7, ACAT2, HSD17B7, MSMO1, HMGCS1,CYP51A1 | Cholesterol biosynthesis I, II, and III | 8.1 | FDFT1, EBP, DHCR7, DHCR24, HSD17B7, MSMO1, CYP51A1 |
| LXR/RXR activation | 7.4 | SCD, APOE, LYZ, ORM1, CCL2, APOC1, IL1B, ORM2, CD14, PTGS2, IL1RAP, TNF, CYP51A1 | Superpathway of gernanylgeranylphosphate Biosynthesis I | 4.4 | FDPS, ACAT2, IDI1, FNTB, HMGCS1 |
| Hepatic fibrosis/hepatic stellate cell activation | 6.1 | CXCL8, APOE, ICAM1, PDGFA, PLA2, G4C, CCR2, F3, LYZ, CCL2, ORM1, APOC1, IL1B, ORM2, PDGFD, TNF | LXR/RXR activation | 4.4 | SCD, FDFT1, LYZ, IL1A, LDLR, IL36RN, NR1H3, IL6, CLU, CYP51A1, IL36B, AGT |
| PPAR signalling | 5.8 | PPARG, JUN, PPARD, PDGFA, MRAS, IL1B, PTGS2,PDGFD, TNF, IL1RAP | Altered T-cell and B-cell signalling in rheumatoid arthritis | 4.3 | IL1A, CSF1, IL36RN, TLR6, TLR8, TLR7, IL6, CSF2, IL36B, IL17A |
| RNA-seq Pat-QKI versus Sib-QKI | RNA-seq Pat-QKI versus Sib-QKI | ||||
| Affected canonical pathway | −Log (P-value) | Affected genes | Affected canonical pathway | −Log (P-value) | Affected genes |
| T-cell receptor signalling | 8.9 | CD247, PTPN7, CAMK4, PRKCQ, CD3E, PLCG1, CD8A, CD3D,CD8B, CD28, CD3G, LCK, TXK, ZAP70, ITK | Granulocyte adhesion and diapedesis | 4.9 | CXCL8, IL1A, HRH2, MMP7, SDC1, PPBP, ITGA6, RDX, CCL24, CCL17, MMP2, CCL22, C5, FPR1, CCL13, ICAM2, IL1RN, MMP19, ITGA4 |
| CCR5 signalling in macrophages | 7.8 | CD247, CD3G, CCR5, CAMK4, PRKCQ, CCL4, CD3E, PLCG2, PLCG1, CCL3, CD3D, GNG10 | Agranulocyte adhesion and diapedesis | 4 | CXCL8, MMP7, IL1A, PPBP, ITGA6, RDX, CCL24, CCL17, MMP2, CCL22, C5, MYL9, CCL13, ICAM2, IL1RN, PODXL, MMP19, ITGA4 |
| Role of NFAT in regulation of the immune response | 7 | CD247, CAMK4, PRKCQ, CD3E, GCER1A, PLCG1, CD3D, GNG10, CD28, CD3G, LCK, GNAT1, PLCG2, ZAP70, FCGR3A/GCGR3B, FCGR1B, ITK | Toll-like receptor signalling | 3 | MAP2K6, IL1A, TICAM2, IL1RN, TLR7, MAPK13, TLR3, IRAK2, TRAF1 |
| EIF2 signalling | 5.8 | RPL24, RPL36A, RPS3A, RPS27, RPL17, RPS18, RPS10, RPL39, RPL12, RPL7A, RPL7, RPL9, RPS28, RPL23A, RPL39L, RPSA | Cysteine biosynthesis/homocysteine degradation | 2.9 | CBS/CBSL, CTH |
| iCOS-iCOSL signalling in T-helper cells | 5.7 | CD247, CD3G, CD28, LCK, CAMK4, PRKCQ, CD3E, ZAP70, PLCG1, CD3D, ICOSLG/LOC102723996, ITK | Axonal guidance signalling | 2.9 | SLIT3, ERAP2, MMP7, SLIT1, PDGFA, SEMA6A, BCAR1, TUBB2B, EPHB1, TUBA8, MYSM1, PRKAR1B, GNB1L, WNT5B, ITGA4, SEMA3G, PAK4, ADAM15, TUBA4A, MMP2, KEL, MYL9, FZD4, ADAM12, SEMA4G, SEMA7A, FZD7 |
IPA, Ingenuity Pathway Analysis; QKI, Quaking.
The top five affected canonical pathways are shown, along with their respective –log(P-value) and the genes that are affected within the particular pathway. Full IPA output is provided in Supplementary Data 7.