Table 2.
DE genes associated with immune and inflammatory responses
| Biological process | Gene symbol | Accession no | Gene description | Fold change |
|---|---|---|---|---|
|
Innate immune response |
MALT1 |
XM_413722 |
mucosa associated lymphoid tissue lymphoma translocation gene 1 |
+2.847583 |
| CLU |
NM_204900 |
clusterin |
+9.196763 |
|
| DMBT1 |
CR353989 |
deleted in malignant brain tumors 1 |
+2.036204 |
|
| DUSP4 |
NM_204838 |
dual specificity phosphatase 4 |
+19.50851 |
|
| DUSP6 |
NM_204354 |
dual specificity phosphatase 6 |
+2.1367393 |
|
| DUSP10 |
NM_001031044 |
dual specificity phosphatase 10 |
+2.5124102 |
|
| LY96 |
BX931181 |
lymphocyte antigen 96 |
+4.2568717 |
|
| SAMHD1 |
NM_001030845 |
SAM domain and HD domain 1 |
+5.7296877 |
|
| ERAP1 |
AJ851612 |
endoplasmic reticulum aminopeptidase 1 |
+5.731377 |
|
| HMGB1 |
NM_204902 |
high mobility group box 1 |
+3.24355 |
|
| TMEM173 |
CR354327 |
transmembrane protein 173 |
+9.81937 |
|
| CFI |
XM_426329 |
complement factor I |
+5.3699164 |
|
| IL1R1 |
NM_205485 |
interleukin 1 receptor, type I |
+2.814695 |
|
| IRAK2 |
NM_001030605 |
interleukin-1 receptor-associated kinase 2 |
+2.1085246 |
|
| IRF7 |
NM_205372 |
interferon regulatory factor 7 |
+4.334887 |
|
| JUN |
NM_001031289 |
jun proto-oncogene |
+3.481312 |
|
| MAP3K14 |
NM_001030927 |
mitogen-activated protein kinase kinasekinase 14 |
+2.0599 |
|
| MYD88 |
NM_001030962 |
myeloid differentiation primary response gene (88) |
+2.0273855 |
|
| NCF2 |
CR391316 |
neutrophil cytosolic factor 2 |
+9.767744 |
|
| NFKB2 |
NM_204413 |
nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100) |
+4.372285 |
|
| MASP1 |
NM_213586 |
mannan-binding lectin serine peptidase 1 (C4/C2 activating component of Ra-reactive factor) |
-5.984035 |
|
| PELI1 |
NM_001012872 |
pellino homolog 1 (Drosophila) |
-2.6004448 |
|
| SIGIRR |
NM_001199542 |
single immunoglobulin and toll-interleukin 1 receptor (TIR) domain |
-3.878401 |
|
| MRPS6 |
NM_001031486 |
mitochondrial ribosomal protein S6 |
-7.8250012 |
|
| IFIH1 |
NM_001193638 |
interferon induced with helicase C domain 1 |
+11.25022 |
|
| SRPK1 |
XM_419265 |
SFRS protein kinase 1 |
+2.4798062 |
|
| TLR4 |
NM_001030693 |
toll-like receptor 4 |
+2.019901 |
|
| TLR5 |
CR353090 |
toll-like receptor 5 |
-2.4051092 |
|
| C1R |
XM_416518 |
complement component 1, r subcomponent |
+13.635473 |
|
| C1S |
NM_001030777 |
complement component 1, s subcomponent |
+16.500757 |
|
| C3 |
NM_205405 |
complement component 3 |
+25.31715 |
|
| C4BPA |
NM_204664 |
complement component 4 binding protein, alpha |
-2.476029 |
|
| C8B |
BX934795 |
complement component 8, beta polypeptide |
-2.8326783 |
|
| TRIM25 |
XM_415653 |
tripartite motif-containing 25 |
+3.5009384 |
|
| COLEC12 |
NM_001039599 |
collectin sub-family member 12 |
-11.011364 |
|
| ITCH |
XM_417330 |
itchy homolog E3 ubiquitin protein ligase (mouse) |
+2.3843937 |
|
| MARCO |
NM_204736 |
macrophage receptor with collagenous structure |
-3.0318317 |
|
| FADD |
XM_421073 |
Fas (TNFRSF6)-associated via death domain |
-2.127713 |
|
| IL18R1 |
NM_001145225 |
interleukin 18 receptor 1 |
+3.5603435 |
|
| VNN1 |
NM_001039288 |
vanin 1 |
+30.900112 |
|
| IL1RL1 |
NM_204275 |
interleukin 1 receptor-like 1 |
-9.989544 |
|
|
Cytokine-mediated signaling pathway |
ADAR |
AM179858 |
adenosine deaminase, RNA-specific |
+2.2560015 |
| USP18 |
CR354286 |
ubiquitin specific peptidase 18 |
+14.18105 |
|
| EGR1 |
CR389000 |
early growth response 1 |
+4.516151 |
|
| IRF8 |
NM_205416 |
interferon regulatory factor 8 |
+4.638908 |
|
| IFI35 |
BX934680 |
interferon-induced protein 35 |
+4.3734093 |
|
| IFNGR1 |
NM_001130387 |
interferon gamma receptor 1 |
+2.4954834 |
|
| IL6 |
NM_204628 |
interleukin 6 (interferon, beta 2) |
+75.02113 |
|
| IL13RA2 |
NM_001048078 |
interleukin 13 receptor, alpha 2 |
+5.0171814 |
|
| IRF1 |
NM_205415 |
interferon regulatory factor 1 |
+7.012157 |
|
| IRF7 |
NM_205372 |
interferon regulatory factor 7 |
+4.334887 |
|
| LIFR |
NM_204575 |
leukemia inhibitory factor receptor alpha |
+2.3569908 |
|
| MX1 |
NM_204609 |
myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse) |
+48.569965 |
|
| NCAM1 |
NM_001242604 |
neural cell adhesion molecule 1 |
-7.5168643 |
|
| IP6K2 |
NM_001030596 |
inositol hexakisphosphate kinase 2 |
+2.4397569 |
|
| PML |
XM_413690 |
promyelocytic leukemia |
+3.3186321 |
|
| ZC3H15 |
NM_001006510 |
zinc finger CCCH-type containing 15 |
-2.916313 |
|
| B2M |
NM_001001750 |
beta-2-microglobulin |
+6.515671 |
|
| PTPN1 |
L20630 |
protein tyrosine phosphatase, non-receptor type 1 |
+3.4228158 |
|
| PTPN2 |
NM_001199387 |
protein tyrosine phosphatase, non-receptor type 2 |
+2.9723573 |
|
| CX3CL1 |
NM_001077232 |
chemokine (C-X3-C motif) ligand 1 |
+10.652483 |
|
| STAT1 |
NM_001012914 |
signal transducer and activator of transcription 1, 91 kDa |
+12.110944 |
|
| STAT3 |
NM_001030931 |
signal transducer and activator of transcription 3 (acute-phase response factor) |
+3.900449 |
|
| VCAM1 |
BX950651 |
vascular cell adhesion molecule 1 |
-2.8632648 |
|
| OASL |
NM_205041 |
2′-5′-oligoadenylate synthetase-like |
+101.55924 |
|
| SOCS1 |
NM_001137648 |
suppressor of cytokine signaling 1 |
+15.976115 |
|
| SOCS3 |
NM_204600 |
suppressor of cytokine signaling 3 |
+30.325502 |
|
| CD44 |
NM_204860 |
CD44 molecule (Indian blood group) |
+5.446098 |
|
| CD74 |
NM_001001613 |
CD74 molecule, major histocompatibility complex, class II invariant chain |
-7.0005507 |
|
| Inflammatory response | CDO1 |
CR353781 |
cysteine dioxygenase, type I |
-6.4660363 |
| CEBPB |
NM_205253 |
CCAAT/enhancer binding protein (C/EBP), beta |
+3.5429432 |
|
| IL23R |
XM_422533 |
interleukin 23 receptor |
+3.9536817 |
|
| EPHX2 |
NM_001033645 |
epoxide hydrolase 2, cytoplasmic |
-2.0498822 |
|
| LY96 |
BX931181 |
lymphocyte antigen 96 |
+4.2568717 |
|
| BLNK |
NM_204908 |
B-cell linker |
+3.781344 |
|
| AOAH |
XM_418835 |
acyloxyacyl hydrolase (neutrophil) |
+3.389245 |
|
| AOX1 |
NM_001038692 |
aldehyde oxidase 1 |
-3.0358417 |
|
| IGFBP4 |
NM_204353 |
insulin-like growth factor binding protein 4 |
-2.5591307 |
|
| IL6 |
NM_204628 |
interleukin 6 (interferon, beta 2) |
+75.02113 |
|
| IRAK2 |
NM_001030605 |
interleukin-1 receptor-associated kinase 2 |
+2.1085246 |
|
| KNG1 |
XM_422766 |
kininogen 1 |
-2.1926415 |
|
| LIPA |
AJ719682 |
lipase A, lysosomal acid, cholesterol esterase (Wolman disease) |
+3.7113423 |
|
| LY75 |
NM_001037836 |
lymphocyte antigen 75 |
+3.9913418 |
|
| NGFB |
M26810 |
nerve growth factor, beta polypeptide |
-2.035398 |
|
| NOX4 |
NM_001101829 |
NADPH oxidase 4 |
-9.4226265 |
|
| F11R |
NM_001083366 |
F11 receptor |
+4.464096 |
|
| GAL |
NM_001159678 |
galaninprepropeptide |
+8.09671 |
|
| SERPINA1 |
BX932103 |
serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1 |
-30.80776 |
|
| S100A9 |
X61200 |
S100 calcium binding protein A9 |
+32.001503 |
|
| CCL4 |
NM_001030360 |
chemokine (C-C motif) ligand 4 |
+10.783558 |
|
| CCL17 |
XM_414018 |
chemokine (C-C motif) ligand 17 |
+4.898831 |
|
| CCL19 |
BX929857 |
chemokine (C-C motif) ligand 19 |
+2.0884924 |
|
| CCL20 |
NM_204438 |
chemokine (C-C motif) ligand 20 |
+4.089286 |
|
| BMP2 |
NM_204358 |
bone morphogenetic protein 2 |
+3.6641774 |
|
| TLR5 |
CR353090 |
toll-like receptor 5 |
-2.4051092 |
|
| TNFAIP6 |
NM_001037837 |
tumor necrosis factor, alpha-induced protein 6 |
+51.35508 |
|
| C3 |
NM_205405 |
complement component 3 |
+25.31715 |
|
| SCG2 |
BX932277 |
secretogranin II (chromogranin C) |
+3.5667899 |
|
| ITCH |
XM_417330 |
itchy homolog E3 ubiquitin protein ligase (mouse) |
+2.3843937 |
|
| VNN1 |
NM_001039288 |
vanin 1 |
+30.900112 |
|
| NMI |
BX950337 |
N-myc (and STAT) interactor |
+3.1200686 |
|
| CHST2 |
XR_027120 |
carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2 |
-2.5672126 |
|
| HDAC9 | CR354257 | histone deacetylase 9 | -6.544272 |
Genes were considered significantly up-regulated or down-regulated if the change in their relative expression levels was ≥ 2-fold or ≤ -2-fold.
The DE genes associated with innate immune response, cytokine-mediated signaling pathway, and inflammatory responses were assigned based on GO term. Most genes could also be classified into other categories, but only innate immune response, cytokine-mediated signaling pathway, and inflammatory responses were considered.
+: up-regulated;-: down-regulated.