Table 1.
Differentially expressed genes (DEGs) between healthy and CVID-affected bone marrow.
| Group comparison | Number of DEG | Over-represented gene term | Fold enrichment | # genes | FDR corrected p-value |
|---|---|---|---|---|---|
| Healthy vs. all CVID | 48 down-regulated | Immunoglobulin C1-set | 337.5 | 7 | 2.88 × 10−9 |
| Genes: IGHD, IGHE, IGHG1, IGHG2, IGHG3, IGHG4, IGKC | |||||
| 55 up-regulated | Chemokine activity | 41.3 | 6 | 3.08 × 10−4 | |
| Genes: CCL4, CCL5, CCL19, CXCL2, CXCL9, IL8 | |||||
| Complement activation | 38.3 | 5 | 1.10 × 10−2 | ||
| Genes: C1R, C1S, C4A, CFH, SERPING1 | |||||
| Healthy vs. CVID group 1 | 71 down-regulated | Blood coagulation | 17.2 | 7 | 4.19 × 10−3 |
| (CVID group 2 not DE) | Genes: CD36, GP6, ITGA2, ITGB3, MMRN1, P2RY12, TREML1 | ||||
| 68 up-regulated | Ectodermal dysplasia | 40.8 | 3 | 2.77 | |
| Genes: KRT6A, KRT14, KRT16 | raw p-value 2.36 × 10 −3 | ||||
| Healthy vs. CVID group 2 | 918 down-regulated | Mitosis | 5.1 | 51 | 1.19 × 10−18 |
| (CVID group 1 not DE) | Genes: ANAPC7, ANLN, ASPM, BUB1B, CCNB1, CCNF, CDC25B, CDCA8, CDK2, CENPE, CENPF, CIT, CKAP5, DLGAP5, ERCC6L, ESPL1, FAM83D, FBXO5, HAUS3, HAUS6, INCENP, KATNB1, KIF2C, KIF15, KIF18A, KIF20B, KIF23, KNTC1, NCAPD2, NCAPD3, NCAPG2, NCAPH, NDC80, NEK2, NUP43, NUSAP1, PBK, PBRM1, PDS5B, RAD21, SGOL1, SMC1A, SMC3, SMC4, SPAG5, STAG2, TERF1, TPX2, TUBB, VCPIP1, WEE1 | ||||
| Kinesin motor region | 6.8 | 12 | 1.34 × 10−3 | ||
| Genes: CENPE, KIF2C, KIF3A, KIF4A, KIF14, KIF15, KIF18A, KIF18B, KIF20A, KIF23, KIF24, KIF27 | |||||
| Heme biosynthetic process | 10.4 | 8 | 8.80 × 10−3 | ||
| Genes: ALAD, ALAS2, CPOX, FECH, FXN, HMBS, PPOX, UROS | |||||
| 1,083 up-regulated | Laminin EGF-like domain | 7.5 | 10 | 6.19 × 10−3 | |
| Genes: HSPG2, LAMA1, LAMA2, LAMA4, LAMB1, LAMB2, LAMC3, NTN1, NTN4, STAB1 | |||||