Brief Article
Copyright ©2010 Baishideng Publishing Group Co.
World J Gastroenterol. Nov 7, 2010; 16(41): 5211-5224
Published online Nov 7, 2010. doi: 10.3748/wjg.v16.i41.5211
Table 1 Primer used for quantitative real-time polymerase chain reaction validation of array results
GeneProbe set IDForwardReverse
CYP4B1M298535'CCGAAGGCTGCAGATGTGT3'5'TTTGGCCCATCCAGAACTAGTAG3'
mSmad75'GGTGCTCAAGAAACTCAAGG3'5'CAGCCTGCAGTCCAGGCG3'
BMP2L02678_at5'TGCCCCCTAGTGCTTCTTAGAC3'5'GGGAAGCAGCAACACTAGAAGAC3'
SGIIIU029835'CAAGCAGGACCGAGAATCAG3'5'CGTTGGACAAGGTCAAGGTG3'
Zfp423U925645'GCAGTGCTACACCTGACTCG3'5'GTCATCCCGCATCTTCTTCTG3'
Pla2g2ax515295'GCTCAATTCAGGTCCAGGG3'5'CCACCCACACCACAATGG3'
EST189231AA7997345'CGGCTCACTGAGCTTGAAGTAG3'5'ACACGACGGAGGAGCTTCTG3'
Olr1AB0059005'CAGAGAGAACTGAAGGAACAG3'5'GGACCTGAAGAGTTTGCAGC3'
ID1L23148_g_at5'TGGACGAACAGCAGGTGAAC3'5'TCTCCACCTTGCTCACTTTGC3'
HK2D26393exon_s_at5'CTCAGAGCGCCTCAAGACAAG3'5'GATGGCACGAACCTGTAGCA3'
Slc16a3U876275'CTCATCGGACCCCCATCAG3'5'CGCCAGGATGAACACATACTTG3'
ratVEGF.15'TGCCAAGTGGTCCCAGGC3'5'ATTGGACGGCAATAGCTGCG3'
Table 2 One hundred genes selected as being differentially expressed after Smad7 overexpression in hepatic stellate cells (note that some specific transcripts are detected by more than one probe set)
Official symbolAverage log2 foldSD log2 foldAffymetrix probe set IDOfficial full name
Downregulated (n = 72)
Acta2-0.850.21X06801cds_i_atSmooth muscle α-actin
Ak3l1-1.200.42rc_AA891949_atAdenylate kinase 3-like 1
Akap12-1.000.57U75404UTR#1_s_atA kinase (PRKA) anchor protein (gravin) 12
Akr1b1-0.700.42M60322_g_atAldo-keto reductase family 1, member B1 (aldose reductase)
Atp6v1b2-1.100.14Y12635_atATPase, H transporting, lysosomal V1 subunit B2
Btg1-0.650.49L26268_g_atB-cell translocation gene 1, anti-proliferative
Clec4f-2.403.39M55532_atC-type lectin domain family 4, member f
Cml5-1.300.42rc_AA894273_atCamello-like 5
Cnn1-1.300.57D14437_s_atCalponin 1
Col1a1-1.510.53M27207mRNA_s_at/rc_AI231472_s_at/U75405UTR#1_f_at/Z78279_at/Z78279_g_atProcollagen, type 1, α 1
Cryab-1.130.32M55534mRNA_s_at/X60351cds_s_atCrystallin, α B
Cyp1b1-1.100.28rc_AI176856_at/U09540_at/U09540_g_atCytochrome P450, family 1, subfamily b, polypeptide 1
Ddah1-0.950.21D86041_atDimethylarginine dimethylaminohydrolase 1
Dpysl2-0.950.64rc_AA875444_atDihydropyrimidinase-like 2
Egr2-1.250.64U78102_atEarly growth response 2
Eif4ebp1-1.050.07U05014_atEukaryotic translation initiation factor 4E binding protein 1
Emp1-0.650.78Z54212_atEpithelial membrane protein 1
Eno2-0.800.71X07729exon#5_s_atEnolase 2, γ
Ercc1-0.750.49rc_AA892791_atExcision repair cross-complementing rodent repair deficiency, complementation group 1
EST (unknown)-2.650.64rc_AI102814_atEST
EST (unknown)-2.600.28rc_AI230256_atEST
EST (unknown)-2.000.14rc_AA874889_g_atEST
EST (unknown)-1.400.85rc_AA866419_atEST
EST (unknown)-1.350.64X62950mRNA_f_atEST
EST (unknown)-1.100.99rc_AA859740_atEST
EST (unknown)-0.850.35rc_AA800708_atEST
EST (unknown)-0.401.41X62951mRNA_s_atEST
F3-1.850.92U07619_atCoagulation factor III
Fabp5-0.800.57S69874_s_atFatty acid binding protein 5, epidermal
Fkbp1a-0.650.49rc_AI228738_s_atFK506 binding protein 1a
Fn1-1.150.36L00190cds#1_s_at/U82612cds_g_at/X05834_atFibronectin 1
Fntb-1.280.49rc_AI136396_at/rc_AI230914_atFarnesyltransferase, CAAX box, β
Gabbr1-1.250.92rc_AI639395_atγ-aminobutyric acid (GABA) B receptor 1
Gpx3-1.100.14D00680_atGlutathione peroxidase 3
Hig1-0.950.49rc_AA891422_atHypoxia induced gene 1
Hk2-3.200.00D26393exon_s_atHexokinase 2
Id1-2.550.35L23148_g_atInhibitor of DNA binding 1
Id2-2.450.21rc_AI137583_atInhibitor of DNA binding 2
Id3-1.850.13AF000942_at/rc_AI009405_s_atInhibitor of DNA binding 3
Idi1-0.700.57AF003835_atIsopentenyl-diphosphate delta isomerase
LOC686781-1.250.21rc_AA799657_atSimilar to NFκB interacting protein 1
Lox-1.100.17rc_AA875582_at/rc_AI234060_s_at/S77494_s_atLysyl oxidase
Lpl-1.200.71L03294_at/L03294_g_at/rc_AI237731_s_atLipoprotein lipase
Lrrc59-0.650.64D13623_atLeucine rich repeat containing 59
Lum-0.800.42X84039_atLumican
Ncam1-1.350.78X06564_atNeural cell adhesion molecule 1
Olr1-2.430.99AB005900_at/AB018104cds_s_at/rc_AI071531_s_atOxidized low density lipoprotein (lectin-like) receptor 1
P4ha1-0.850.21X78949_atProcollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), α 1 polypeptide
Pcsk6-1.100.71rc_AI230712_atProprotein convertase subtilisin/kexin type 6
Pfkp-1.250.54L25387_at/L25387_g_atPhosphofructokinase, platelet
Plaur-1.200.71X71898_atPlasminogen activator, urokinase receptor
Plod2-1.000.28rc_AA892897_atProcollagen lysine, 2-oxoglutarate 5-dioxygenase 2
Pmepa1-1.550.07rc_AI639058_s_atProstate transmembrane protein, androgen induced 1
Ptk2-0.850.35S83358_s_atPTK2 protein tyrosine kinase 2
Rasl11a-2.250.49rc_AI169372_atRAS-like family 11 member A
Rasl11b-1.030.24rc_AA800853_at/rc_AA800853_g_atRAS-like family 11 member B
Rcn2-0.900.57U15734_atReticulocalbin 2
RGD1306841-1.100.14rc_AI639203_atSimilar to RIKEN cDNA 2410006F12
RGD1310444_predicted-1.250.21rc_AA866432_atLOC363015 (predicted)
Rgs4-1.450.64U27767_atRegulator of G-protein signaling 4
Sc4mol-1.100.45E12625cds_at/rc_AI172293_atSterol-C4-methyl oxidase-like
Schip1-1.000.42rc_AA800036_atSchwannomin interacting protein 1
Serpine1-1.900.00M24067_atSerine (or cysteine) peptidase inhibitor, clade E, member 1
Slc12a2-0.800.99AF051561_s_atSolute carrier family 12, member 2
Slc16a3-2.050.35U87627_atSolute carrier family 16 (monocarboxylic acid transporters), member 3
Slc2a1-1.150.35S68135_s_atSolute carrier family 2 (facilitated glucose transporter), member 1
Spink8-2.551.48rc_AA799734_atSerine peptidase inhibitor, kazal type 8
Tfrc-0.900.42M58040_atTransferrin receptor
Tnc-0.900.28U09401_s_atTenascin C
Tnnt2-1.700.42M80829_atTroponin T2, cardiac
Vegfa-2.251.28L20913_s_at/M32167_g_at/rc_AA850734_atVascular endothelial growth factor A
Wfdc1-1.700.14AF037272_atWAP four-disulfide core domain 1
Up-regulated (n = 28)
Adora2a0.850.35S47609_s_atAdenosine A2a receptor
Agtr1a0.950.21M74054_s_at/X62295cds_s_atAngiotensin II receptor, type 1 (AT1A)
Bmp22.831.31L02678_at/rc_AA997410_s_atBone morphogenetic protein 2
Col3a10.900.42M21354_s_at/X70369_s_at/Procollagen, type III, α 1
Cxcl101.050.21U17035_s_atChemokine (C-X-C motif) ligand 10
Cyp2e11.000.14M20131cds_s_atCytochrome P450, family 2, subfamily e, polypeptide 1
Cyp4b13.250.49M29853_atCytochrome P450, family 4, subfamily b, polypeptide 1
Ednrb0.700.42rc_AA818970_s_atEndothelin receptor type B
Ephx11.150.21M26125_atEpoxide hydrolase 1, microsomal
EST (unknown)0.800.28rc_AA874873_g_atEST
EST (unknown)0.900.28rc_AI177256_atEST
Glul0.900.23M91652complete_seq_at/rc_AA852004_s_atGlutamate-ammonia ligase (glutamine synthase)
Hgf1.030.05E03190cds_s_at/X54400_r_atHepatocyte growth factor
Hsd11b10.950.49rc_AI105448_atHydroxysteroid 11-β dehydrogenase 1
Igfbp31.150.30M31837_atInsulin-like growth factor binding protein 3
Kif41.050.07rc_AA859926_atKinesin family member 4
Lhx20.950.21L06804_atLIM homeobox protein 2
Notch10.800.42X57405_g_atNotch gene homolog 1 (Drosophila)
Nr2f10.950.21U10995_g_atNuclear receptor subfamily 2, group F, member 1
Pdcd41.000.14rc_AI172247_atProgrammed cell death 4
Pdgfra1.100.28rc_AI232379_atPlatelet derived growth factor receptor, α polypeptide
Pla2g2a3.600.00X51529_atPhospholipase A2, group IIA (platelets, synovial fluid)
Ptn2.100.57rc_AI102795_atPleiotrophin
Scg32.700.85U02983Secretogranin III
Serping10.850.21rc_AA800318_atSerine (or cysteine) peptidase inhibitor, clade G, member 1
Smad75.351.20AF042499_atMAD homolog 7 (Drosophila)
Sod31.050.07Z24721_atsuperoxide dismutase 3, extracellular
Zfp4231.851.47U92564_at/U92564_g_atZinc finger protein 423
Table 3 Comparison of gene regulation in activated hepatic stellate cells in vivo (De Minicis et al[13])
Gene symbolSmad7 overexpressing HSCsIn vivo activated untransformed HSCs
Acta2
BMP21
Cnn1
Col1a1
Col3a1
Cryab
Cyp1b1
Ddah1
Ednrb2
Eno2
Ephx12
Fn1
Gabbr1
Hgf2
Hk21
Hsd11b12
Id1
Igfbp32
Kif4
Lox
Lpl2
Lum
Ncam1
P4ha1
Pdgfra
Pfkp
Plod2
Rasl11b
Serping1
Slc16a3
Slc2a1
Sod3
Tmepai_predicted2
Tnc2
Tnnt2
VEGFa1↑ (VEGFc)1
Wfdc12
Table 4 Comparison of gene regulation according to quantitative real-time polymerase chain reaction analysis and array analysis
GeneProbe set IDArrayRT-PCR analysis
Cyp4B1M29853_atUpUp
Smad7AF042499_atUpUp
BMP2L02678_at/rc_AA997410_s_atUpUp
SGIIIU02983_atUpUp
Zfp423U92564_at/U92564_g_atUpUp
Pla2g2ax51529_atUpUp
EST189231AA799734_atDownDown
Olr1AB005900_at/ AB018104cds_s_at/ rc_AI071531_s_atDownDown
ID1L23148_g_atDownDown
HK2D26393exon_s_atDown3 d down/7 d up
Slc16a3U87627_atDown3 d down/7 d up
VEGFa/ratVEGF.1 in RT-PCRL20913_s_at/M32167_g_atDown3 d down/7 d up