Table 3.
Differentially expressed genes between lake and river populations also found as differentially expressed in previous parasite infection studies
| Gene ID | Gene name | Comparisons in Lenz et al. 2013, a | Tissue in Lenz et al. 2013 | Log fold‐change in Lenz et al. 2013, b | Tissue in this study | Log fold‐change in this studyc | FDR in this study |
|---|---|---|---|---|---|---|---|
| ENSGACG00000011746 |
fyco1a
FYVE and coiled‐coil domain containing 1a |
Control vs. infected | Head kidney | −3.21 | Head kidney | 0.71 | 0.0096 |
| ENSGACG00000010806 |
sox7
SRY‐box containing gene 7 |
Control vs. infected | Head kidney | −2.58 | Head kidney | 0.74 | 0.038 |
| ENSGACG00000013129 | MRPL49 (2 of 2) mitochondrial ribosomal protein L49 | Control vs. infected | Head kidney | −2.69 | Head kidney | −0.91 | 0.017 |
| ENSGACG00000015653 |
lmo1
LIM domain only 1 |
Control vs. infected | Head kidney | −1.20 | Head kidney | 1.13 | 0.033 |
| ENSGACG00000014705 |
mettl13
Methyltransferase‐like 13 |
Lake vs. River in 2nd infection; control vs. infected | Head kidney | −4.4 and −2.69 | Spleen | −0.63 | 0.028 |
| ENSGACG00000011977 |
ppdpfa
Pancreatic progenitor cell differentiation and proliferation factor a |
Control vs. infected | Head kidney | 1.03 | Spleen | 3.17 | 0.011 |
| ENSGACG00000001923 |
n6amt2
N‐6 adenine‐specific DNA methyltransferase 2 |
Control vs. infected | Head kidney | 1.56 | Spleen | −0.88 | 0.025 |
| ENSGACG00000004515 |
Cfd
Complement factor D (adipsin) |
Control vs. infected | Head kidney | −1.48 | Spleen | 1.16 | 0.00065 |
| ENSGACG00000012609 | LGALS1 (2 of 3) lectin, galactoside binding, soluble, 1 | Control vs. infected | Head kidney | −5.09 | Spleen | 0.73 | 0.0038 |
| ENSGACG00000011683 |
slc5a6b
Solute carrier family 5, member 6 |
Control vs. infected | Head kidney | −2.46 | Spleen | −0.45 | 0.045 |
| Gene ID | Gene name | Comparisons in Haase et al. 2014, a | Tissue in Haase et al. 2014 | Log fold‐change in Haase et al. 2014, b | Tissue in this study | Log fold‐change in this studyc | FDR |
|---|---|---|---|---|---|---|---|
| ENSGACG00000003716 | CASQ2 (1 of 2) calsequestrin 2 | Control vs. clone XII | Head kidney | 2.8 | Spleen | −0.97 | 0.0080 |
| ENSGACG00000017615 |
Smox
Spermine oxidase |
Control vs. clone I, control vs. XII and control vs. clone mix | Head kidney | 4.79, 5.81 and 5.11 | Spleen | 0.65 | 0.011 |
| ENSGACG00000011977 |
ppdpfa
Pancreatic progenitor cell differentiation and proliferation factor a |
Control vs. clone I | Head kidney | −4.08 | Spleen | 3.17 | 0.011 |
| ENSGACG00000004966 | IRF4 (2 of 2) interferon regulatory factor 4b | Control vs. clone I, control vs. XII and control vs. clone mix | Head kidney | 1.41, 2.26 and 1.79 | Spleen | −0.59 | 0.028 |
| ENSGACG00000020628 |
angptl5
Angiopoietin‐like 5 |
Control vs. clone mix | Head kidney | 2.83 | Spleen | 0.71 | 0.028 |
| ENSGACG00000017656 | SVIL (2 of 2) supervillin | Control vs. clone mix | Head kidney | 2.96 | Spleen | 0.59 | 0.040 |
| ENSGACG00000008510 |
apnl
Actinoporin‐like protein |
Control vs. clone mix | Gill | −1.20 | Head kidney and spleen | 0.88 and 1.05 | 0.0093 and 0.0030 |
For the DE genes Haase et al. 2014 identified in gill, only the overlapped DE genes we identified in both head kidney and spleen are shown.
Comparisons where the genes were previously identified as differentially expressed are indicated. In Lenz et al. 2013; DE gene sets between control naïve fish from lake and from river, between twice exposed fish from lake and from river (2nd infection), and between infected fish and control fish were compared to DE gene sets in this study. In Haase et al. 2014, DE gene sets between control fish and infected fish with different parasite clones were compared.
In lake‐river comparisons, positive log fold‐change values represent higher expression in lake fish and vice versa. In control‐infection comparisons, positive values represent upregulation with infection compared to control.
Positive log fold‐change values represent higher expression in lake fish and vice versa.