Table 2

Top canonical pathways and corresponding genes modulated by Padma 28 in HepG2 cells
Microarray (n=1) RT-PCR (n=5)
Pathway/Gene Gene title log2 (ratio) Fold Fold P(H1)
Metabolism of xenobiotics by cytochrome P450 (p-value: 3.82E-05; ratio: 10/178)
CYP1A1 cytochrome P450, family 1, subfamily A1 8.7 408.4 123.4 ± 31.1 0.001
PTGR1 prostaglandin reductase 1 4.8 27.9
GSTA1 glutathione S-transferase alpha 1 2.6 6.1 4.5 ± 1.3 0.036
AKR1C2 aldo-keto reductase family 1, member C2 2.4 5.3 6.7 ± 1.2 0.007
AKR1C1 aldo-keto reductase family 1, member C1 2.1 4.3 6.7 ± 1.2 0.007
CYP4F11 cytochrome P450, family 4, subfamily F 11 1.7 3.2
MGST1 microsomal glutathione S-transferase 1 1.6 3.0
ALDH1L1 aldehyde dehydrogenase 1 family, member L1 1.6 3.0 4.1 ± 1.0 0.003
EPHX1 epoxide hydrolase 1, microsomal 1.3 2.5
CYP2S1 cytochrome P450, family 2, subfamily S1 1.2 2.2 5.1 ± 1.5 0.018
Glutathione metabolism (p-value: 4,01E-04; ratio 7/92)
GSTA1 glutathione S-transferase alpha 1 2.6 6.1 4.5 ± 1.3 0.036
GCLM glutamate-cysteine ligase, modifier subunit 2.1 4.1
GCLC glutamate-cysteine ligase, catalytic subunit 1.7 3.3 5.8 ± 0.9 0.009
MGST1 microsomal glutathione S-transferase 1 1.6 3.0
GPX2 glutathione peroxidase 2 1.2 2.3 0.3 ± 0.9 0.881
RAB15 RAB15, member RAS onocogene family 1.1 2.1
IDH3A isocitrate dehydrogenase 3 (NAD+) alpha 1.1 2.1
Aminoacyl-tRNA biosynthesis (p-value: 4.24E-04; ratio 6/83)
CARS cysteinyl-tRNA synthetase 2.1 4.3 3.2 ± 0.6 0.001
YARS tyrosyl-tRNA synthetase 1.3 2.5
WARS tryptophanyl-tRNA synthetase 1.2 2.4 3.8 ± 1.0 0.020
GARS glycyl-tRNA synthetase 1.2 2.3
AARS alanyl-tRNA synthetase 1.2 2.3
MARS methionyl-tRNA synthetase 1.1 2.2
LPS/IL-1 mediated inhibition of RXR function (p-value: 1.82E-03; ratio 12/205)
GSTA1 glutathione S-transferase alpha 1 2.6 6.1 4.5 ± 1.3 0.036
CD14 CD14 molecule 2.4 5.3
ABCC4 ATP-binding cassette, sub-family C, member 4 2.1 4.3
ABCC3 ATP-binding cassette, sub-family C, member 3 1.8 3.5
MGST1 microsomal glutathione S-transferase 1 1.6 3.0
ALDH1L1 aldehyde dehydrogenase 1 family, member L1 1.6 3.0 4.1 ± 1.0 0.003
NR1H3 nuclear receptor subfamily 1, group H, member 3 1.5 2.8
ALDH1A1 aldehyde dehydrogenase 1 family, member A1 1.3 2.5
SLC35A2 solute carrier family 35, member A2 1.1 2.1
SULT1E1 sulfotransferase family 1E, member 1 -1.3 -2.5
SLCO1B3 solute carrier organic anion transporter 1B3 -1.3 -2.5
FMO5 flavin containing monooxygenase 5 -1.9 -3.7
Nrf2-mediated oxidative stress response (p-value: 2.92E-03; ratio 11/181)
GSTA1 glutathione S-transferase alpha 1 2.6 6.1 4.5 ± 1.3 0.036
HMOX1 heme oxygenase (decycling) 1 2.1 4.3 5.3 ± 0.8 0.008
GCLM glutamate-cysteine ligase, modifier subunit 2.1 4.3
GCLC glutamate-cysteine ligase, catalytic subunit 1.7 3.3 5.8 ± 0.9 0.009
NQO1 NAD(P)H dehydrogenase, quinone 1 1.7 3.2
MGST1 microsomal glutathione S-transferase 1 1.6 3.0
EPHX1 epoxide hydrolase 1, microsomal (xenobiotic) 1.3 2.5
FTH1 ferritin, heavy polypeptide 1 1.3 2.5
TXNRD1 thioredoxin reductase 1 1.3 2.5
GPX2 glutathione peroxidase 2 (gastrointestinal) 1.2 2.3 0.3 ± 0.9 0.881
SLC35A2 solute carrier family 35 , member A2 1.1 2.1
Aryl Hydrocarbon Receptor Signaling (p-value: 4.65E-03; ratio 9/150)
CYP1A1 cytochrome P450, family 1, subfamily A1 8.7 408.4 123.4 ± 31.1 0.001
GSTA1 glutathione S-transferase alpha 1 2.6 6.1 4.5 ± 1.3 0.036
NQO1 NAD(P)H dehydrogenase, quinone 1 1.7 3.2
FAS Fas (TNF receptor superfamily, member 6) 1.7 3.2
MGST1 microsomal glutathione S-transferase 1 1.6 3.0
ALDH1L1 aldehyde dehydrogenase 1 family, member L1 1.6 3.0 4.1 ± 1.0 0.003
ALDH1A1 aldehyde dehydrogenase 1 family, member A1 1.3 2.5
SLC35A2 solute carrier family 35, member A2 1.1 2.1
NCOA2 nuclear receptor coactivator 2 -1.1 -2.1

The p-value is a measure of the probability of the association of a specific pathway and the dataset. The ratio indicates the number of molecules in a given pathway from the input dataset that meet the cut-off criteria (fold change of 2) divided by the number of molecules that make up that pathway in the database.

Klein et al.

Klein et al. BMC Genomics 2013 14:133   doi:10.1186/1471-2164-14-133

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