Uniquely Active Gene at 2 Weeksa

Fold Change Based on Microarray

Analysisb

qRT-PCR Data

Mean Fold Change in PB-treated Groupc

No. of animals above upper limit of 95% CI of

control groupd

No. of animals below lower limit of 95% CI of

control groupd

B6 C57 B6 C57 B6 C57 B6 C57

Abcc2e 2.01 -- ↑ 1.76 ↑ 1.57 6 6 0 0

Abcc3f 3.03 -- ↑ 2.51 ↑ 1.53 6 6 0 0

Baxg 2.77 -- n.c. n.c. 3 1 0 2

Casp3 2.28 -- n.c. n.c. 4 3 0 2

Cbsf -2.13 -- ↓ -2.28 ↓ -1.31 0 0 6 5

Cebpb 3.12 -- ↑ 3.81 n.c. 6 1 0 0

Cldn1f -3.07 -- ↓ -4.45 ↓ -2.06 0 0 6 6

Ctgfe 2.86 -- ↑ 2.98 ↑ 2.26 6 6 0 0

Dnmt3bf -2.56 -- ↓ -6.60 ↓ -4.08 0 0 6 6

Gadd45bh 2.00 -- ↑ 4.28 ↑ 2.60 6 6 0 0

Id3e -2.33 -- ↓ -1.71 ↓ -1.56 0 0 5 6

Lcn2 5.91 -- n.c. ↑ 1.58 2 4 0 0

Prdm2g -2.18 -- n.c. n.c. 0 1 4 2

Pxr 2.22 -- ↑ 1.43 n.c. 6 0 0 0

Shc1 2.35 -- n.c. n.c. 0 0 3 0

Shmt1g 2.03 -- n.c. n.c. 3 0 0 1

Slco1a4f,+ 3.52 -- ↑ 2.96 ↑ 1.33 6 5 0 0

Tnfsf10 2.56 -- ↑ 1.26 n.c. 6 0 0 0

Supplementary Table S4. Quantitative real-time PCR (qRT-PCR) analysis of the expression of 18 genes that were uniquely active in livers of B6C3F1 mice at 2 weeks of phenobarbital (PB) treatment

aSeventeen uniquely active genes observed in livers of B6C3F1 mice only at 2 weeks, a subset of the 234 identified based on microarray analysis (as described in the Methods), were chosen for confirmation of their expression statuses by qRT-PCR. Additionally, 1 (of the 47 total) uniquely active carry forward genes (i.e. its induction or repression was observed in the B6C3F1 at both 2 and 4 weeks), indicated by the plus sign (+), was assayed at 2 weeks. bFold changes of gene expression are expressed as a change in a phenobarbital (PB)-treated group v. its time-matched control (up-regulation, ↑ or down-regulation, ↓). Those that are highlighted in yellow were confirmed, or apparently confirmed, by qRT-PCR (as described in the Methods). (--) indicates that a gene was not active. cAll fold changes listed are statistically significant in a PB-treated group v. its time-matched control (Student’s t-test, p < 0.05). No change (n.c.) indicates that the fold change was not significant. dThe 95% confidence interval (CI) of the control group data was calculated, and the number of samples (out of 6 total) from a PB-treated group that fell outside the 95% CI are listed. Highlighted in blue are those circumstances where data from at least 3 of the samples that fell outside the 95% CI of the control group data were considered an ‘indication of a change’, thus apparently confirming the microarray data (see footnote ‘g’). eExpression was not confirmed, since the fold changes in the B6C3F1 and C57BL/6 mice were not statistically different (Student’s t-test, p < 0.05).fExpression was confirmed, since the fold changes in the B6C3F1 and C57BL/6 mice were statistically different (Student’s t-test, p < 0.05).gExpression was apparently confirmed. hExpression was apparently confirmed. The level of expression in the B6C3F1 appears to be higher than that seen in the C57BL/6; however, this does not reach statistical significance due to a particularly low level of expression in one of the B6C3F1 mice.

Footnotes - Supplementary Table S4.

Uniquely Active Gene at 4 Weeksa

Fold Change Based on Microarray Analysisb

qRT-PCR Data

Mean Fold Change in PB-treated Groupc

No. of animals above upper limit of 95% CI of control groupd

No. of animals below lower limit of 95% CI of

control groupd

B6 C57 B6 C57 B6 C57 B6 C57

Alas1 8.12 -- ↑ 4.57 ↓ -3.14 6 0 0 6

Ephb4 2.24 -- ↓ -1.25 n.c. 0 0 4 1

Gadd45a 4.27 -- ↑ 2.32 n.c. 6 0 0 0

Map2k6 2.16 -- ↑ 1.70 n.c. 4 1 0 0

Map3k5e 2.79 -- n.c. ↓ -1.20 4 0 0 4

Mtrr 4.48 -- ↑ 1.43 ↓ -1.36 6 0 0 6

Plk3e 5.85 -- n.c. ↓ -4.99 3 0 2 6

Ppargc1a 2.34 -- n.c. n.c. 1 1 1 2

Shp -2.51 -- ↓ -1.94 n.c. 0 2 3 0

Slco1a4f,+ 2.14 -- ↑ 1.64 ↑ 1.56 4 5 0 0

Wee1 3.05 -- ↑ 3.72 n.c. 5 0 0 1

Supplementary Table S5. Quantitative real-time PCR (qRT-PCR) analysis of the expression of 11 genes that were uniquely active in livers of B6C3F1 mice at 4 weeks of phenobarbital (PB) treatment

Footnotes - Supplementary Table S5.

aTen uniquely active genes observed in livers of B6C3F1 mice only at 4 weeks, a subset of the 86 identified based on microarray analysis (as described in the Methods), were chosen for confirmation of their expression statuses by qRT-PCR. Additionally, 1 (of the 47 total) uniquely active carry forward genes (i.e. its induction or repression was observed in the B6C3F1 at both 2 and 4 weeks), indicated by the plus sign (+), was assayed at 4 weeks. bFold changes of gene expression are expressed as a change in a phenobarbital (PB)-treated group v. its time-matched control (up-regulation, ↑ or down-regulation, ↓). Those that are highlighted in yellow were confirmed, or apparently confirmed, by qRT-PCR. (--) indicates that a gene was not active. cAll fold changes listed are statistically significant in a PB-treated group v. its time-matched control (Student’s t-test, p < 0.05). No change (n.c.) indicates that the fold change was not significant. dThe 95% confidence interval (CI) of the control group data was calculated, and the number of samples (out of 6 total) from a PB-treated group that fell outside the 95% CI are listed. Highlighted in blue are those circumstances where data from at least 3 of the samples that fell outside the 95% CI of the control group data were considered an ‘indication of a change’, thus apparently confirming the microarray data (see footnote ‘e’). eExpression was apparently confirmed. fExpression was not confirmed, since the fold changes in the B6C3F1 and C57BL/6 mice were not statistically different (Student’s t-test, p < 0.05).

Genes that enhance growth, survival, angiogenesis, invasion, metastasisb

Genes that suppress growth, survival, angiogenesis, invasion, metastasisb

↑c ↓c ↓c ↑c

Totalsd (out of 234 unique

B6C3F1, 2-week genes)

32 g = 23, a = 7, m = 4,

s = 18, i = 6

15 g = 13, a = 1, m = 2,

s = 4, i = 3

12 g = 9, a = 1, m = 0,

s = 7, i = 0

33 g = 21, a = 3, m = 3,

s = 22, i = 5

Ddit4 (s) Blnk (g,s)

Kcnk5 (s) Sp3 (g)

Gpr182 (g,i) Hmox1(g,s)

Ccne2 (g) Shc1 (g,s,a)

Cebpb (g,s) Pfn1 (g)

Tk1 (g) Pscd1 (g)

Ngef (g) Cxcr7 (g,s,a,i,m)

Ctgf (g,a,i,m) Aqp1 (g,a,i,m)

Slc37a4 (s,i) Gabpa (g)

Gnpnat1 (g) Shmt1 (g)

Hyal1 (g,a) Brap (s)

Tnfsf10 (s,a,i) Pctp (s)

Angptl4 (s,a,m) Fkbp5 (g,s)

Gadd45b (g,s) Mknk2 (g,s)

Dclre1a (s) St3gal5 (g)

Pex11b (s) Pik3ap1 (g,s)

Pde4b (s)

Crip2 (g)

Eml4 (g)

Zfp36l1 (g)

Lrp5 (g,i)

Map3k7ip2 (s)

Id3 (g,a,m)

Dnmt3b (g)

Pkhd1 (g,s)

Cldn1 (g,i,m)

Inhba (g)

Pdgfc (g)

Clock (g)

Insig2 (g,s,i)

Pnkd (g)

Zfp36l1 (s,a)

March7 (g)

Ppp2r4 (s)

Prdm2 (g,s)

Irf6 (g)

Cgn (g)

Id3 (g,s)

Cabc1 (g,s)

Bach2 (g,s)

Inhba (g)

Nedd41 (s)

Pkhd1 (g)

Lcn2 (s,i,m) Tnfsf10 (s,a)

Tsc22d3 (g,s) Blnk (g)

Ddit4 (g) Fbxo31 (g)

Kcnk5 (s) Dpp8 (s)

Cebpb (g,s) Errfi1 (g)

Pctk3 (g,s) Pik3ap1 (g)

Saa1 (g,s) Trim24 (g)

Ak2 (s) Dnajb4 (g,i)

Dclre1a (g) Shc1 (s)

Ctgf (g,s,a,i,m) Pfn1 (g,i)

Bax (g,s) Gmnn (g,s)

Cebpd (g) Casp3 (s)

Rarb (g,s) Bri3 (s)

Gnpnat1 (s) Acads (s)

Hyal1 (g,s) Saa2 (g,s)

Angptl4 (g,a,i,m) Gadd45b (s)

Pklr (s)

Totalsd (out of 47 carry forward

B6C3F1 genes)

9 g = 7, a = 0, m = 0,

s = 5, i = 0

2 g = 1, a = 1, m = 0,

s = 1, i = 1

1 g = 1, a = 0, m = 0,

s = 0, i = 0

5 g = 5, a = 0, m = 0,

s = 4, i = 0

D0H4S114 (g) Pfkfb3 (g)

Dnaja1 (s) Pim3 (g,s)

Hspa1b (s) Ppat (g)

Nrg4 (g) Sh3bp2 (g,s)

Pbef1 (g,s)

Ddah1 (g,a)

Tff3 (s,i)

Tff3 (g) Arl6ip5 (g,s)

Fhit (g,s)

Morc3 (g)

Per1 (g,s)

Per2 (g,s)

Totalsd (out of 281 unique B6C3F1, 2-week genes)

41 g = 30, a = 7, m = 4,

s = 23, i = 6

17 g = 14, a = 2, m = 2,

s = 5, i = 4

13 g = 10, a = 1, m = 0,

s = 7, i = 0

38 g = 26, a = 3, m = 3,

s = 26, i = 5

Supplementary Table S6. Connections between 5 cancer-related processes and genes, including those which carried forward,

that were uniquely active in the B6C3F1 mice following treatment with phenobarbital (PB) for 2 weeksa

Footnotes - Supplementary Table S6

aUniquely active genes in livers of B6C3F1 mice at 2 weeks, including those that carried forward (i.e. exhibited similar expression changes, either induction of repression, at both 2 and 4 weeks), were identified as described in the Methods. Quantitiative real-time PCR (qRT-PCR) was performed on a subset of these (see Supplementary Table S4 for the complete data set), denoted here in bolded font, and genes whose expression changes were confirmed are underlined. bFunctional annotation revealed associations between key cancer-related processes (growth: g, survival: s, angiogenesis: a, invasion: i, and metastasis: m) and many of the 281 total uniquely active genes at 2 weeks, which include genes observed only at 2 weeks, in yellow, plus carry forward genes, in green. cGene symbols are listed in a particular column based on whether the literature indicates that the gene enhances or suppresses a particular process, and genes are further classified depending on whether their expression is induced (↑) or repressed (↓) by PB treatment. Note that a gene which suppresses growth or survival can do so by promoting apoptosis and/or cell death. dThe total number of genes in each of the specific categories is depicted in bold. Those totals not listed in bold represent the genes, within a category, that can participate in one or more cancer-related processes.

Genes that enhance growth, survival, angiogenesis, invasion, metastasisb

Genes that suppress growth, survival, angiogenesis, invasion, metastasisb

↑c ↓c ↓c ↑c

Totalsd (out of 86 unique B6C3F1, 4-week genes)

16 g = 8, a = 3, m = 1,

s = 9, i = 3

3 g = 3, a = 0, m = 0,

s = 1, i = 0

6 g = 5, a = 0, m = 0,

s = 3, i = 0

15 g = 10, a = 1, m = 1,

s = 11, i = 3

Hsph1 (g,s) Mafb (g,s)

Thrsp (g,s) Dnajb9 (s)

Plk3 (g) Ppargc1a (a)

Ptp4a1 (g,i,m) Rnd3 (s)

Bhlhb2 (s) Ephb4 (g,s,a,i)

Wee1 (s) Bach1 (g)

Map3k5 (a) Map2k6 (i)

Tesk2 (s) Atp6v0a2 (g)

Fdft1 (g,s)

Fgl1 (g)

Arntl (g)

Ppap2c (s)

Grk5 (g)

Fgl1 (g)

Nr0b2/Shp (g,s)

Tsc22d1 (g)

Osgin1 (g,s)

Efhd2 (s) Ephb4 (g,s,i)

Plk3 (g,s) Map3k5 (s)

Gadd45a (g,s) Hsph1 (s)

Rnd3 (g,s) Mafb (g)

Bhlhb2 (s) Map2k6 (g,s,i,m)

Wee1 (g) Mme (g,a,i)

Ppargc1a (s) Atp6v0a2 (g)

Klf10 (g,s)

Totalsd (out of 47 carry forward B6C3F1 genes)

9 g = 7, a = 0, m = 0,

s = 5, i = 0

2 g = 1, a = 1, m = 0,

s = 1, i = 1

1 g = 1, a = 0, m = 0,

s = 0, i = 0

5 g = 5, a = 0, m = 0,

s = 4, i = 0

D0H4S114 (g) Pfkfb3 (g)

Dnaja1 (s) Pim3 (g,s)

Hspa1b (s) Ppat (g)

Nrg4 (g) Sh3bp2 (g,s)

Pbef1 (g,s)

Ddah1 (g,a)

Tff3 (s,i)

Tff3 (g) Arl6ip5 (g,s)

Fhit (g,s)

Morc3 (g)

Per1 (g,s)

Per2 (g,s)

Totalsd (out of 133 unique

B6C3F1, 4-week genes)

25 g = 15, a = 3, m = 1,

s = 14, i = 3

5 g = 4, a = 1, m = 0,

s = 2, i = 1

7 g = 6, a = 0, m = 0,

s = 3, i = 0

20 g = 15, a = 1, m = 1,

s = 15, i = 3

Supplementary Table S7. Connections between 5 cancer-related processes and genes, including those which carried forward,

that were uniquely active in the B6C3F1 mice following treatment with phenobarbital (PB) for 4 weeksa

Footnotes - Supplementary Table S7

aUniquely active genes in livers of B6C3F1 mice at 4 weeks, including those that carried forward (i.e. exhibited similar expression changes, either induction of repression, at both 2 and 4 weeks), were identified as described in the Methods. Quantitiative real-time PCR (qRT-PCR) was performed on a subset of these (see Supplementary Table S5 for the complete data set), denoted here in bolded font, and genes whose expression changes were confirmed are underlined. bFunctional annotation revealed associations between key cancer-related processes (growth: g, survival: s, angiogenesis: a, invasion: i, and metastasis: m) and many of the 133 total uniquely active genes at 4 weeks, which include genes observed only at 4 weeks, in orange, plus carry forward genes, in green. cGene symbols are listed in a particular column based on whether the literature indicates that the gene enhances or suppresses a particular process, and genes are further classified depending on whether their expression is induced (↑) or repressed (↓) by PB treatment. Note that a gene which suppresses growth or survival can do so by promoting apoptosis and/or cell death. dThe total number of genes in each of the specific categories is depicted in bold. Those totals not listed in bold represent the genes, within a category, that can participate in one or more cancer-related processes.