| Functions | Genes | Exposed tissues | Exposed to | References |
| Reference genes | 18S, Rpl7, and β-actin | | | |
| Hypoxia-responsive | Telomerase reverse transcriptase (Tert) | Ovary, liver, testis, kidney, gill, brain, spleen, intestine, eye, muscle, and skin | Hypoxia | [16, 22] | Hypoxia-inducible factor-1α (Hif 1α) | Liver, testis | Hypoxia | [22] | Erythropoietin (Epo) | Liver, testis, and embryos | Hypoxia, PFOS | [22, 23] | Leptin receptor (Lepr) | Liver, gill, heart, kidney, gill, brain, spleen, intestine, eye, muscle, ovary, and testis | Hypoxia | [24] | Hemoxygenase-1 (Ho) | Liver, gill, and heart | WAFs, Hypoxia | [24, 25] |
| Immune toxicity | Glutathione peroxidase (Gpx) | Embryos | PFOS | [26] | Catalase (Cat) | Embryos | PFOS | [26] | Uncoupling protein 2 (Ucp2) | Embryos | PFOS | [26, 27] | Cyclooxygenase-2 (Cox2) | Embryos | PFOS | [26] | Peroxisome proliferator-activated receptors(Ppars): Pparα, Pparβ, and Pparγ | Embryos, whole fish | PFOS, WAFs | [25, 26, 28] |
| Complement-related genes | Lectin, mannose-binding 2 (Mbl2) | Liver | PBDE-47 | [29] | Cyan fluorescent protein (Cfp) | Liver | PBDE-47 | [29] | Complement component: C1r/s, C3, C9, C3-2, C4, C1q, C5, C8, C1 inhibitor | Liver | PBDE-47, Vibrio parahaemolyticus | [29, 30] | Prothrombin (F2) | Liver | | [30] | Complement factor: Hf, Bf | Liver | Vibrio parahaemolyticus | [30] | Hepcidin (Hep): Hep1, Hep2 | Liver, spleen, gill, intestine, ovary, testis, brain, and embryos | Vibrio parahaemolyticus | [30] | Mannose-binding lectin-associated serine protease (Masp) | Liver | Vibrio parahaemolyticus | [30] |
| Inflammation-related genes | Tumor necrosis factor-α (Tnfα) | Embryos | PFOS, BPA | [26, 31] | Interleukin (Il): Il1β, Il8 | Embryos | PFOS, BPA | [26, 31] | CC chemokine eotaxin-1 (Ccl11) | Embryos | BPA | [31] | Superoxide dismutase (Sod) | Embryos | PFOS, BPA | [26, 31] |
| Osmoregulatory mechanism | Na+/K+-ATPase (Nka) | Gill, embryos | BPA, SW (35), BW (15), and FW (0) | [7, 31, 32] | Na+, K+, 2Cl− cotransporter (Nkcc): Nkcc1a, Nkcc1b, and Nkcc2 | Gill, liver, testis, intestine, ovary, brain, muscle, kidney, heart, Fin, and eye | SW (35), BW (15), and FW (0) | [32] | FXYD domain-containing ion transport regulator (Fxyd): Fxyd5, Fxyd6, Fxyd7, Fxyd8, Fxyd9, Fxyd11, and Fxyd12 | Gill, intestine, kidney, brain, eye, liver, and caudal fin | SW (35), BW (15), FW (0) | [5] |
| Cardiac development-related genes | NK2 transcription factor related 5 (Nkx2.5) | Embryos | PFOS, BPA | [23, 31] | Cyclooxygenase (Cox): Cox1, Cox2 | Embryos | PFOS, BPA | [23, 31] | ATP synthase | Embryos | PFOS | [23, 27] | Bone morphogenetic protein (Bmp4) | Embryos | PFOS, BPA | [23, 31] | Fibroblast growth factor 8 (Fgf8) | Embryos | PFOS, BPA | [23, 31] | GATA-binding protein 4 (Gata4) | Embryos | PFOS, BPA | [23, 31] | Leptin receptor (Lerp) | Embryos | BPA | [31] | SET and MYND domain containing 1 (Smyd1) | Embryos | PFOS | [23] |
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Metabolisms | Cytochrome P450 (Cyps) | Liver, gill, embryos, intestine, and ovary | PFOS, WAFs | [25, 28, 33] | Aldehyde dehydrogenase (Aldh) | | WAFs | [25] | Glutathione S-transferase (Gst): Gsta, Gstk, Gsto, Gstt, and Gstz | | WAFs | [25] | Sulfotransferase (Sult): Sult1, Sult2 cytosolic, Sult2b1, Sult2b2, Sult3 cytosolic, Sult3-like, Sult4a1, and Sult6b1 | | WAFs | [25] | UDP-glucuronyltransferases (Ugts): Ugt1b, Ugt2a, Ugt2a2, Ugt2a3, Ugt2b33, Ugt2b3-like, Ugt5a1, and Ugt5g1 | | WAFs | [25] | Hydroxysteroid dehydrogenase (Hsd): 3β-Hsd, 11 β-Hsd, and 17β-Hsd | | WAFs | [25] | Aryl Hydrocarbon Receptor (Ahr): Ahr1, Ahr2 | Embryos, whole fish | PFOS, WAFs | [25, 28] | 5 α-reductase (Srd5a) | | WAFs | [25] | Steroidogenic acute regulatory protein (Star) | | WAFs | [25] | ATP-binding cassette (Abc): Abcb1, Abcc2, Abcc3, Abcc4, and Abcg2 | | WAFs | [25] | Heat shock protein (Hsp): Hsp10, Hsp22, Hsp27, Hsp30, Hsp60, Hsp70, Hsp75, Hsp90a, Hsp90β, Hspβ7, and Hspβ11 | | WAFs | [25] | Choriogenin H and L (Chgh and Chgl) | Liver, embryos, and larvae | PFOS, E2, EE2, BPA, and NP | [28, 34] | Kinesin superfamily7 (Kif7) | Brain, kidney, liver, muscle, ovary, and testicle | | [6] | Aryl hydrocarbon receptor nuclear translocator (Arnt) | Embryos | PFOS | [28] | Vitellogenin (Vtg) | Embryos, liver, gill, intestine | PFOS | [28] | Estrogen receptor (Er) | Embryos | PFOS | [28] | Horiolysin H and L (Hce and Lce) | Embryos | PFOS | [10] |
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