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Table 2 Differentially expressed genes (DEGs) identified in each tissue

From: Mitonuclear mismatch alters nuclear gene expression in naturally introgressed Rhinolophus bats

DEGs Log2CPM Log2FC p-adj Gene description
Pectoral muscle     
DNASE1L3 1.42 6.63 8.90E−04 Deoxyribonuclease 1 like 3
CLNK 0.20 5.85 7.96E−03 Cytokine dependent hematopoietic cell linker
ACTC1 5.35 5.41 5.00E−03 Actin alpha cardiac muscle 1
TNNT2 0.58 5.40 2.39E−03 Troponin T2, cardiac type
CXCL10 1.89 4.92 2.47E−06 C-X-C motif chemokine ligand 10
SLAMF6 0.90 4.32 2.18 E−02 SLAM family member 6
IL21R 1.72 4.19 2.71E−02 Interleukin 21 receptor
VPREB3 1.09 3.97 2.58E−02 V-set pre-B cell surrogate light chain 3
CD3G 1.76 3.88 1.44E−03 CD3g molecule
XCL1 1.27 3.87 1.97E−03 X-C motif chemokine ligand 1
CD7 2.06 3.50 1.70E−03 CD7 molecule
WDFY4 3.50 3.41 2.12E−05 WDFY family member 4
IRF8 2.83 3.41 1.95E−03 Interferon regulatory factor 8
CPVL 3.52 3.37 1.44E−03 Carboxypeptidase vitellogenic like
MYL4 2.80 3.32 3.52E−03 Myosin light chain 4
RYR3 2.68 3.22 9.62E−03 Ryanodine receptor 3
LCK 3.16 3.07 1.32E−02 LCK proto-oncogene, Src family tyrosine kinase
PRUNE2 0.97 3.00 4.15E−02 Prune homolog 2 with BCH domain
XIRP2 7.30 2.90 2.96E−02 xin actin binding repeat containing 2
CD3E 2.67 2.87 4.46E−02 CD3e molecule
IL2RB 2.27 2.82 5.73E−03 interleukin 2 receptor subunit beta
LAT 1.52 2.76 2.71E−02 Linker for activation of T cells
MPEG1 3.08 2.68 1.44E−03 Macrophage expressed 1
ITM2A 2.31 2.48 2.03E−02 Integral membrane protein 2A
CTSW 2.13 2.37 2.03E−02 Cathepsin W
CILP 3.51 2.20 1.44E−03 Cartilage intermediate layer protein
GPX3 5.21 2.02 8.05E−03 Glutathione peroxidase 3
CD74 7.86 1.92 5.70E−03 CD74 molecule
ARHGAP22 1.81 1.92 7.96E−03 Rho GTPase activating protein 22
SYNPO2 5.17 1.90 7.96E−03 Synaptopodin 2
HLA-DRA 6.85 1.81 2.06E−02 Major histocompatibility complex, class II, DR alpha
POSTN 2.44 1.76 1.16E−02 Periostin
PLIN1 5.38 1.69 4.16E−02 Perilipin 1
MFAP5 2.23 1.64 4.22E−02 Microfibril associated protein 5
COL1A2 4.44 1.47 4.22E−02 Collagen type I alpha 2 chain
MAP1A 3.59 1.39 8.05E−03 Microtubule associated protein 1A
HSPB6 7.15 1.27 7.96E−03 Heat shock protein family B (small) member 6
SLC16A5 5.94 − 1.11 2.96E−02 Solute carrier family 16 member 5
CATSPER2 2.06 − 1.54 2.71E−02 Cation channel sperm associated 2
CSF3R 3.68 − 2.39 5.73E−03 Colony stimulating factor 3 receptor
CYP4F2 3.20 − 2.69 1.21E−02 Cytochrome P450 family 4 subfamily F member 2
IL1B 3.72 − 2.82 7.96E−03 Interleukin 1 beta
CCL8 2.16 − 3.30 2.83E−03 C–C motif chemokine ligand 8
Heart     
ISG15 3.31 1.69 2.67E−06 ISG15 ubiquitin like modifier
IFI6 5.41 1.64 3.03E−04 Interferon alpha inducible protein 6
Brain     
CYP26A1 5.46 1.83 1.35E−05 Cytochrome P450 family 26 subfamily A member 1
CFHR3 0.56 − 5.08 1.35E−03 Complement factor H related 3
Liver     
HLA-A 7.78 1.14 3.68E−02 HLA class I histocompatibility antigen, A alpha chain
SULT2A1 7.12 − 1.18 4.36E−05 Sulfotransferase family 2A member 1
ANKH 3.35 − 1.19 4.34E−03 ANKH inorganic pyrophosphate transport regulator
SPP1 5.18 − 1.87 3.99E−02 Secreted phosphoprotein 1
WFDC2 3.27 − 2.04 1.73E−02 WAP four-disulfide core domain 2
RGS4 0.72 − 2.57 3.73E−02 Regulator of G-protein signaling 4
TGM1 3.24 − 3.04 2.08E−07 Protein-glutamine gamma-glutamyltransferase K
Cochlea     
SCTR 2.97 2.00 8.05E−04 Secretin receptor
SLC40A1 4.64 1.13 7.06E−03 Solute carrier family 40 member 1
MYOC 7.71 − 1.94 8.99E−03 Myocilin
Small intestine     
CA3 3.63 3.13 8.11E−03 Carbonic anhydrase 3
NMRAL1 2.36 1.33 2.11E−02 NmrA-like family domain containing 1
PCDH8 3.36 − 2.32 1.38E−05 Protocadherin 8
  1. Positive and negative values indicate that genes are upregulated and downregulated in mismatched group, respectively. CPM and FC indicate counts per million and fold change, respectively