Table 1 The shared and specific DEGs in Manila clam post injected with LPS, PGN and poly (I:C)
Abbreviations | Gene name | ID | Log2 Fold change | ||
|---|---|---|---|---|---|
LPS vs PBS | PGN vs PBS | poly(I:C) vs PBS | |||
DEGs shared by all three group | |||||
MUCL | Mucin-like protein | evm.model.xfSc0001058.9 | 25.53 | 24.04 | 14.51 |
IFI | Interferon alpha-inducible protein 27 | evm.model.xfSc0000070.25 | 10.58 | 11.38 | 3.46 |
CTRP3 | Complement C1q tumor necrosis factor-related protein 3 | evm.model.xfSc0000125.38 | 10.34 | 9.58 | 24.80 |
Perlucin | Perlucin | Novel03513 | 10.15 | 8.12 | 8.95 |
CALM | Calmodulin | evm.model.xfSc0002618.1 | 6.73 | 6.67 | 2.56 |
LC | Snaclec coagulation factor IX | evm.model.xfSc0030245.1 | 6.60 | 5.24 | 22.74 |
DEF | Defensin | Novel05650 | 4.90 | 8.49 | 11.01 |
PGRP | Peptidoglycan recognition protein | Novel01511 | 4.73 | 2.75 | 8.01 |
ITGA | Integrin alpha-4 | Novel02605 | 3.64 | 6.31 | 5.72 |
IFI | Interferon alpha-inducible protein 27 like protein 1 | evm.model.xfSc0000188.23 | −23.45 | −4.62 | −5.44 |
GBP1 | Interferon-induced guanylate-binding protein 1-like | Novel04750 | −22.62 | −23.78 | − 23.09 |
GTPA | GTP-binding protein A | evm.model. Sc0000135.12 | −9.97 | −9.08 | −9.72 |
RNF213 | E3 ubiquitin-protein ligase RNF213 | evm.model.xfSc0002255.2 | −9.80 | −5.56 | −13.83 |
NPC2 | Epididymal secretory protein E1 | evm.model.xfSc0001403.6 | −9.46 | − 10.00 | − 9.22 |
HCK | Tyrosine-protein kinase HCK | evm.model. Sc0000062.24 | −8.90 | −4.42 | −22.62 |
ITGB | Integrin beta-like protein A | Novel03831 | −7.15 | −11.42 | −5.63 |
Ubr2 | E3 ubiquitin-protein ligase | evm.model.xfSc0002514.1 | −6.90 | −5.70 | −10.69 |
HAAF | Hemagglutinin/amebocyte aggregation factor | Novel05234 | −6.71 | −2.32 | −2.01 |
LRIG1 | Leucine-rich repeats and immunoglobulin-like domains protein1 | evm.model. Sc0000048.11 | −6.16 | −4.85 | −4.57 |
Ubr1 | E3 ubiquitin-protein ligase | Novel07244 | −6.06 | −5.34 | −6.68 |
DAPK1 | Death-associated protein kinase 1 | evm.model.xfSc0000378.13 | −4.94 | −6.66 | −5.17 |
GBP1 | Interferon-induced guanylate-binding protein 1 | Novel02352 | −4.67 | −5.99 | −9.27 |
DEGs shared by LPS and PGN group | |||||
DEFB | Defensin-B | evm.model.xfSc0000150.16 | 26.78 | 26.33 | Â |
CDH23 | Cadherin-23 | evm.model.xfSc0000164.15 | 10.73 | 10.79 | Â |
HEXB | Beta-hexosaminidase subunit beta | evm.model.xfSc0006767.1 | 8.71 | 9.95 | Â |
NEK7 | Serine/threonine-protein kinase Nek7-like | Novel08087 | 8.22 | 8.64 | Â |
CALM | Calmodulin | evm.model.xfSc0000392.15 | 8.14 | 8.33 | Â |
LR74A | Leucine-rich repeat-containing protein 74A | evm.model.xfSc0000002.29 | 7.56 | 8.65 | Â |
CRIP2 | Cysteine-rich protein 2 | evm.model.xfSc0001224.15 | 5.90 | 6.92 | Â |
GM2 | Ganglioside GM2 activator | evm.model.xfSc0000725.12 | 5.86 | 6.19 | Â |
Nim1k | Serine/threonine-protein kinase NIM1 | evm.model.xfSc0000017.35 | 5.53 | 6.12 | Â |
LR74A | Leucine-rich repeat-containing protein 74A | evm.model.xfSc0000002.30 | 5.51 | 5.36 | Â |
TEX14 | Serine/threonine-protein kinase TEX14 | evm.model.xfSc0000164.11 | 5.20 | 5.64 | Â |
CNR3 | Cell number regulator 3 | evm.model.xfSc0001389.2 | 4.97 | 4.89 | Â |
CSA1 | Cell surface antigen I/II | evm.model.xfSc0000741.1 | 4.80 | 4.25 | Â |
TBA3 | Tubulin alpha-3 chain | evm.model.xfSc0000328.3 | 4.79 | 4.76 | Â |
CATH | Cathelicidin-B1 | evm.model.xfSc0001753.3 | 4.65 | 4.09 | Â |
SRCR | Scavenger receptor cysteine-rich | evm.model.xfSc0004748.1 | 4.54 | 4.30 | Â |
LSS | Lysostaphin | evm.model.xfSc0000599.7 | 4.35 | 4.73 | Â |
FCGR | Low affinity immunoglobulin epsilon Fc receptor-like | Novel02789 | 3.78 | 7.03 | Â |
DYH8 | Dynein heavy chain 8 | evm.model. Sc0000012.11 | 3.68 | 5.54 | Â |
FCGBP | IgGFc-binding protein | evm.model.xfSc0000000.12 | −9.374 | −8.78 |  |
C1qL | Complement C1q-like protein 4 | evm.model.xfSc0010046.1 | −7.39 | −5.44 |  |
CTRP3 | Complement C1q tumor necrosis factor-related protein 3 | evm.model.xfSc0001711.7 | −2.30 | −10.37 |  |
FA10 | Coagulation factor X | evm.model.xfSc0000836.3 | −2.17 | −8.98 |  |
CTL | C-type lectin | evm.model.xfSc0000570.24 | 1.50 | −2.74 |  |
DEGs shared by LPS and poly(I:C) group | |||||
C1qL | Complement C1q-like protein 4 | evm.model.xfSc0000421.27 | 8.80 | Â | 23.06 |
CELSR1 | Cadherin EGF LAG seven-pass G-type receptor 1 | evm.model.xfSc0000749.1 | 8.27 | Â | 25.47 |
THAP12 | 52 kDa repressor of the inhibitor of the protein kinase-like | Novel02627 | 8.06 |  | 10.93 |
HSP70A | Heat shock 70 kDa protein 12A | evm.model.xfSc0002157.2 | 4.54 |  | 4.51 |
C3 | Complement component C3 | Novel05951 | 2.99 | Â | 3.61 |
TGFBI | Transforming growth factor-beta-induced protein ig-h3 | evm.model.xfSc0003432.2 | −10.37 |  | −10.09 |
HSP70 | Heat shock 70 kDa protein | evm.model.xfSc0000048.21 | −6.45 |  | −7.55 |
CL12 | Collectin-12 | evm.model.xfSc0000743.13 | −5.99 |  | 1.37 |
ADGRE1 | Adhesion G protein-coupled receptor E1 | evm.model.xfSc0003876.2 | −5.77 |  | −1.13 |
DEGs shared by PGN and poly(I:C) group | |||||
RNF213 | E3 ubiquitin-protein ligase RNF213 | Novel00498 | Â | 25.70 | 13.53 |
MMR1 | Macrophage mannose receptor 1 | evm.model.xfSc0000262.8 | Â | 5.43 | 4.06 |
PGRP | Peptidoglycan recognition protein | evm.model.xfSc0000442.9 | Â | 4.39 | 1.25 |
TLR2 | Toll-like receptor 2 | Novel05810 | Â | 3.13 | 8.62 |
GBP1 | Interferon-induced guanylate-binding protein 1-like | Novel03779 |  | −25.11 | −24.42 |
Casp3 | Caspase-3 | Novel00341 |  | −6.27 | −3.42 |
FAS1 | Fasciclin-1-like isoform X2 | Novel05543 |  | −4.89 | −9.62 |
DD2 | Discoidin-2 | Novel04420 |  | −4.57 | −25.07 |
LTL | L-type lectin | evm.model.xfSc0004145.1 |  | −3.01 | −10.70 |
Secific DEGs of LPS group | |||||
SPI | Serine protease inhibitor Cvsi-2-like | Novel07619 | 12.47 | Â | Â |
FCN1 | Ficolin-1 | evm.model.xfSc0000006.29 | 9.42 | Â | Â |
DYLC6 | Dynein light chain LC6 | evm.model.xfSc0000411.8 | 9.33 | Â | Â |
HSP70B | Heat shock 70 kDa protein 12B | evm.model.xfSc0003908.3 | 9.10 |  |  |
IMSP3 | Insoluble matrix shell protein 3 | evm.model.xfSc0000186.20 | 8.98 | Â | Â |
IMSP3 | Insoluble matrix shell protein 3 | evm.model. Sc0000176.1 | 5.71 | Â | Â |
IMSP1 | Insoluble matrix shell protein 1 | evm.model.xfSc0000058.28 | 4.40 | Â | Â |
PAR14 | Poly [ADP-ribose] polymerase 14 | evm.model.xfSc0003656.1 | −24.49 |  |  |
PO | Peroxidase-like protein | evm.model.xfSc0000759.9 | −4.32 |  |  |
Specific DEGs of PGN group | |||||
HSP70B | Heat shock 70 kDa protein 12B | evm.model.xfSc0002250.4 |  | 22.30 |  |
HAAF | Hemagglutinin/amebocyte aggregation factor | Novel08154 | Â | 10.22 | Â |
PYG | Glycogen phosphorylase | evm.model.xfSc0001103.7 | Â | 8.58 | Â |
HSP70B | Heat shock protein 70 B2 | evm.model.xfSc0000005.7 | Â | 8.87 | Â |
DYH8 | Dynein heavy chain 8 | evm.model. Sc0000012.12 | Â | 5.87 | Â |
TLR1 | Toll-like receptor 1 | evm.model.xfSc0000331.15 |  | −7.86 |  |
PAR14 | Poly [ADP-ribose] polymerase 14 | evm.model.xfSc0001993.2 |  | −6.92 |  |
CO8A | Collagen alpha-1(VIII) chain | evm.model.xfSc0000095.25 |  | −4.87 |  |
RNF213 | E3 ubiquitin-protein ligase RNF213 | evm.model.xfSc0003464.1 |  | −3.61 |  |
Specific DEGs of poly(I:C) group | |||||
Siglec | Sialic acid-binding lectin | Novel06415 | Â | Â | 24.00 |
FCGR | Low affinity immunoglobulin epsilon Fc receptor | evm.model.xfSc0000236.23 | Â | Â | 23.86 |
IFI | Interferon-induced protein 44-like | evm.model.xfSc0004748.1 | Â | Â | 11.07 |
FREP | Fibrinogen-like protein A | evm.model.xfSc0000316.4 | Â | Â | 10.07 |
IFI | Interferon-inducible GTPase 5-like | Novel03245 | Â | Â | 5.10 |
IFI44 | Interferon-induced protein 44 | evm.model.xfSc0003071.3 |  |  | −25.60 |
PAR12 | Poly [ADP-ribose] polymerase 12 | evm.model.xfSc0000879.10 |  |  | −24.32 |
CAPRIN2 | Caprin-2 | evm.model.xfSc0001617.5 |  |  | −9.18 |
LRR | Leucine-rich repeat protein, putative | Novel03097 |  |  | −5.82 |