Table 1

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

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

5.09c

-1.52

Cytochrome P450 1A1 (EC 1.14.14.1) (CYP1A)_1115

1.29

4.82b, c

-1.12

*UnAn_29411_6378 (CYP1B1)

-1.03

4.61b, c

-2.51

T-cell surface glycoprotein CD3 delta chain precursor (T-cell receptor T3 delta chain)_3770

1.14

2.92b, c

-1.64

*UnAn_27910_5543 (CYP1B1)

1.22

2.54b, 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

1.84b, c

1.02

Small inducible cytokine A4 homolog precursor (Macrophage inflammatory protein 1-beta homolog)_3581

1.13

1.78c

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

11.78a, c

1.12

Cytochrome P450 1A1 (EC 1.14.14.1) (CYP1A)_1115

1.10

6.10a, c

-1.13

T-cell surface glycoprotein CD3 delta chain precursor (T-cell receptor T3 delta chain)_3770

1.07

5.47a, c

-1.25

*UnAn_27910_5543 (CYP1B1)

-1.02

3.36a, 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

3.00c

-1.03

**UnAn_29159_6257 (apolipoprotein E)

1.18

2.66c

-1.20

**UnAn_28041_5632 (apolipoprotein E)

1.02

2.43c

-1.01

Acidic phosphoprotein precursor (50 kDa antigen)_277

1.11

2.37c

-1.15

**UnAn_23610r_4780 (apolipoprotein E)

1.06

2.30c

-1.45

UnAn_21996_4295

-1.15

2.09a, c

-1.01

Apomucin (Mucin core protein) (Fragment)_492

1.16

2.02c

1.45

C61 protein [Mus musculus]_684

1.22

1.99c

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

1.90c

-1.24

MHC class II transactivator (CIITA)_2363

1.03

1.76c

-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

2.13c

Type II antifreeze protein precursor (AFP)_4059

-1.12

-1.30

1.72c

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

-1.55c

1.30

RWD domain containing protein 1 (Small androgen receptor-interacting protein)_3458

1.05

-1.73

-1.05

Parvalbumin beta_2778

1.30

-1.80c

-1.49


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.

*These two probes represent the same transcript, which has been annotated as cytochrome P450 1B1 (CYP1B1) using data from 454 libraries.

** These three probes represent the same transcript, which has been annotated as apolipoprotein E using data from 454 libraries.

aAlso differentially expressed at 5 dpf.

bAlso differentially expressed at 10 dpf.

cAlso differentially expressed at 15 dpf.

Oleksiak et al. BMC Genomics 2011 12:263   doi:10.1186/1471-2164-12-263

Open Data