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Table 1 Differential gene expression and PCB inducibility in pairwise comparisons of NBH and SC embryos at 5 and 10 dpf.

From: Transcriptomic assessment of resistance to effects of an aryl hydrocarbon receptor (AHR) agonist in embryos of Atlantic killifish (Fundulus heteroclitus) from a marine Superfund site

Gene NBH PCB/NBH DMSO SC PCB/SC DMSO NBH DMSO/SC DMSO
5 days post fertilization    
basic leucine zipper nuclear factor 1 [Mus musculus]_603 -1.03 5.09 c -1.52
Cytochrome P450 1A1 (EC 1.14.14.1) (CYP1A)_1115 1.29 4.82 b, c -1.12
*UnAn_29411_6378 (CYP1B1) -1.03 4.61 b, c -2.51
T-cell surface glycoprotein CD3 delta chain precursor (T-cell receptor T3 delta chain)_3770 1.14 2.92 b, c -1.64
*UnAn_27910_5543 (CYP1B1) 1.22 2.54 b, c -1.32
Diablo homolog, mitochondrial precursor (Second mitochondria-derived activator of caspase) (Smac protein) (Direct IAP binding protein with low pI)_1191 -1.03 2.40 2.14
UnAn_21996_4295 1.28 1.84 b, c 1.02
Small inducible cytokine A4 homolog precursor (Macrophage inflammatory protein 1-beta homolog)_3581 1.13 1.78 c 1.03
Synaptophysin-like protein (Pantophysin)_3753 -1.15 1.43 1.64
ATP synthase lipid-binding protein, mitochondrial precursor (EC 3.6.3.14) (ATP synthase proteolipid P2) (ATPase protein 9) (ATPase subunit C)_560 1.79 1.31 1.47
Hypothetical protein C31G5.21 in chromosome I_1963 1.12 1.27 1.98
hect domain and RLD 4 isoform b [Homo sapiens]_1806 1.33 1.21 -1.06
UnAn_26723_4896 -1.14 1.14 2.12
UnAn_23246_4614 -1.09 1.03 1.96
UnAn_22726_4401 1.03 -1.10 1.88
Proteasome subunit beta type 7 precursor (EC 3.4.25.1) (Proteasome subunit Z) (Macropain chain Z) (Multicatalytic endopeptidase complex chain Z)_3109 1.41 -1.10 -1.14
Deoxyribonuclease-1 precursor (EC 3.1.21.1) (Deoxyribonuclease I) (DNase I)_1181 1.48 -1.14 -2.57
Guanidinoacetate N-methyltransferase (EC 2.1.1.2)_1754 -1.16 -1.25 -3.28
10 days post fertilization    
*UnAn_29411_6378 (CYP1B1) 1.09 11.78 a, c 1.12
Cytochrome P450 1A1 (EC 1.14.14.1) (CYP1A)_1115 1.10 6.10 a, c -1.13
T-cell surface glycoprotein CD3 delta chain precursor (T-cell receptor T3 delta chain)_3770 1.07 5.47 a, c -1.25
*UnAn_27910_5543 (CYP1B1) -1.02 3.36 a, c -1.29
Tubulointerstitial nephritis antigen-like precursor (Androgen-regulated gene protein 1) (Adrenocortical zonation factor 1) (AZ-1) (Tubulointersititial nephritis antigen-related protein) (TARP)_4042 1.49 3.00 c -1.03
**UnAn_29159_6257 (apolipoprotein E) 1.18 2.66 c -1.20
**UnAn_28041_5632 (apolipoprotein E) 1.02 2.43 c -1.01
Acidic phosphoprotein precursor (50 kDa antigen)_277 1.11 2.37 c -1.15
**UnAn_23610r_4780 (apolipoprotein E) 1.06 2.30 c -1.45
UnAn_21996_4295 -1.15 2.09 a, c -1.01
Apomucin (Mucin core protein) (Fragment)_492 1.16 2.02 c 1.45
C61 protein [Mus musculus]_684 1.22 1.99 c 1.84
WAP four-disulfide core domain protein 3 precursor (Putative protease inhibitor WAP14)_6790 1.02 1.96 1.59
Tyrosine aminotransferase (EC 2.6.1.5) (L-tyrosine:2-oxoglutarate aminotransferase) (TAT)_4064 -1.14 1.90 c -1.24
MHC class II transactivator (CIITA)_2363 1.03 1.76 c -1.06
UnAn_23121_4564 -1.09 1.75 1.54
Troponin C, slow skeletal and cardiac muscles (TN-C)_3995 1.08 1.63 2.68
Epsin-4 (Epsin-related protein) (EpsinR) (Enthoprotin)_1384 1.38 1.62 2.03
UnAn_27985_5592 -1.10 1.44 1.13
AMP deaminase 1 (EC 3.5.4.6) (Myoadenylate deaminase) (AMP deaminase isoform M)_431 1.27 1.43 1.49
UnAn_29343_6349 1.20 1.31 1.48
UnAn_29849_6655 1.11 1.24 1.67
Cathepsin D precursor (EC 3.4.23.5)_755 -1.45 1.04 1.01
UnAn_22785_4432 -1.24 -1.01 -1.84
UnAn_20648_4152 1.32 -1.05 1.01
Mitogen-activated protein kinase kinase 1 interacting protein 1 (MEK binding partner 1) (Mp1)_2424 -1.10 -1.07 -1.51
Epididymal secretory glutathione peroxidase precursor (EC 1.11.1.9) (Epididymis-specific glutathione peroxidase-like protein) (EGLP)_1378 -1.73 -1.15 -1.32
Muted protein homolog_2461 -1.60 -1.16 -1.50
UnAn_22879_4456 1.56 -1.20 -1.51
UnAn_22354_4332 -1.09 -1.28 2.13 c
Type II antifreeze protein precursor (AFP)_4059 -1.12 -1.30 1.72 c
T-cell surface glycoprotein CD8 beta chain precursor (CD8 antigen 37 kDa chain) (OX-8 membrane antigen)_3771 1.51 -1.32 -1.12
UnAn_20957_4180 -1.84 -1.32 -1.48
Chromobox protein homolog 2 (Modifier 3 protein) (M33)_827 -1.65 -1.47 -1.36
Beta enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (Muscle-specific enolase) (MSE) (Skeletal muscle enolase) (Enolase 3)_620 -1.00 -1.53 -1.29
UnAn_27466_5284 1.30 -1.54 -1.33
Transcription factor PU.1_3890 1.19 -1.55 -1.36
UnAn_22873_4452 -1.00 -1.55 c 1.30
RWD domain containing protein 1 (Small androgen receptor-interacting protein)_3458 1.05 -1.73 -1.05
Parvalbumin beta_2778 1.30 -1.80 c -1.49
  1. Genes with significant differences in pairwise comparisons of gene expression at 5 and 10 dpf are included. (For 15-dpf data, see Additional file 4: Table S2.) Gene expression ratios are indicated. A gene with a positive fold-difference is more highly expressed in the population/treatment listed first, and a gene with a negative fold-difference is more highly expressed in the population/treatment listed last. Genes are listed in order of ratios in the reference population (SC) comparison with tolerant population (SC). Ratios with significant p-values are in bold. See Table S1 ( Additional file 2) for a list of all genes significant in the ANOVA analysis. NBH: New Bedford Harbor; SC: Scorton Creek; PCB: PCB-126; DMSO: dimethylsulfoxide. Unannotated genes are denoted by UnAn and a unique number. Some of the unannotated probes were subsequently annotated after extension using the 454 database; see Table S4 ( Additional file 6) for details.
  2. *These two probes represent the same transcript, which has been annotated as cytochrome P450 1B1 (CYP1B1) using data from 454 libraries.
  3. ** These three probes represent the same transcript, which has been annotated as apolipoprotein E using data from 454 libraries.
  4. aAlso differentially expressed at 5 dpf.
  5. bAlso differentially expressed at 10 dpf.
  6. cAlso differentially expressed at 15 dpf.