Skip to main content

Table 1 The shared and specific DEGs in Manila clam post injected with LPS, PGN and poly (I:C)

From: New insights into the Manila clam and PAMPs interaction based on RNA-seq analysis of clam through in vitro challenges 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  
CDH23 Cadherin-23 evm.model.xfSc0000164.15 10.73 10.79  
HEXB Beta-hexosaminidase subunit beta evm.model.xfSc0006767.1 8.71 9.95  
NEK7 Serine/threonine-protein kinase Nek7-like Novel08087 8.22 8.64  
CALM Calmodulin evm.model.xfSc0000392.15 8.14 8.33  
LR74A Leucine-rich repeat-containing protein 74A evm.model.xfSc0000002.29 7.56 8.65  
CRIP2 Cysteine-rich protein 2 evm.model.xfSc0001224.15 5.90 6.92  
GM2 Ganglioside GM2 activator evm.model.xfSc0000725.12 5.86 6.19  
Nim1k Serine/threonine-protein kinase NIM1 evm.model.xfSc0000017.35 5.53 6.12  
LR74A Leucine-rich repeat-containing protein 74A evm.model.xfSc0000002.30 5.51 5.36  
TEX14 Serine/threonine-protein kinase TEX14 evm.model.xfSc0000164.11 5.20 5.64  
CNR3 Cell number regulator 3 evm.model.xfSc0001389.2 4.97 4.89  
CSA1 Cell surface antigen I/II evm.model.xfSc0000741.1 4.80 4.25  
TBA3 Tubulin alpha-3 chain evm.model.xfSc0000328.3 4.79 4.76  
CATH Cathelicidin-B1 evm.model.xfSc0001753.3 4.65 4.09  
SRCR Scavenger receptor cysteine-rich evm.model.xfSc0004748.1 4.54 4.30  
LSS Lysostaphin evm.model.xfSc0000599.7 4.35 4.73  
FCGR Low affinity immunoglobulin epsilon Fc receptor-like Novel02789 3.78 7.03  
DYH8 Dynein heavy chain 8 evm.model. Sc0000012.11 3.68 5.54  
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   23.06
CELSR1 Cadherin EGF LAG seven-pass G-type receptor 1 evm.model.xfSc0000749.1 8.27   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   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   25.70 13.53
MMR1 Macrophage mannose receptor 1 evm.model.xfSc0000262.8   5.43 4.06
PGRP Peptidoglycan recognition protein evm.model.xfSc0000442.9   4.39 1.25
TLR2 Toll-like receptor 2 Novel05810   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   
FCN1 Ficolin-1 evm.model.xfSc0000006.29 9.42   
DYLC6 Dynein light chain LC6 evm.model.xfSc0000411.8 9.33   
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   
IMSP3 Insoluble matrix shell protein 3 evm.model. Sc0000176.1 5.71   
IMSP1 Insoluble matrix shell protein 1 evm.model.xfSc0000058.28 4.40   
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   10.22  
PYG Glycogen phosphorylase evm.model.xfSc0001103.7   8.58  
HSP70B Heat shock protein 70 B2 evm.model.xfSc0000005.7   8.87  
DYH8 Dynein heavy chain 8 evm.model. Sc0000012.12   5.87  
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    24.00
FCGR Low affinity immunoglobulin epsilon Fc receptor evm.model.xfSc0000236.23    23.86
IFI Interferon-induced protein 44-like evm.model.xfSc0004748.1    11.07
FREP Fibrinogen-like protein A evm.model.xfSc0000316.4    10.07
IFI Interferon-inducible GTPase 5-like Novel03245    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