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Table 6 Shift-probe sequences

From: Genome wide prediction of HNF4α functional binding sites by the use of local and global sequence context

Gene symbol*

Gene name†

Oligo-name‡

Location (rel.TSS)§

Score

Sequence¥

TCF1/HNF1

hepatic nuclear factor 1

HNF1

-265

0.988

AAGGCTGAAGTCCAAAGTTCAGTCCCTTC

APOB

Apolipoprotein B

APOB

-86

0.905

GGAAAGGTCCAAAGGGCGCCTTG

SERPINA1/AAT

alpha-1-antitrypsin

GS21

-134

0.865

CAACAGGGGCTAAGTCCACTGGC

AGT

angiotensinogen

GS47

-429

0.905

TGCAGAGGGCAGAGGGCAGGGGA

APOC3

Apolipoprotein C3

GS104

-93

0.995

GGCGCTGGGCAAAGGTCACCT GC

CYP2D6

cytochrome P450, family 2, subfamily D, polypeptide 6

GS105

-69

0.989

AGCAGAGGGCAAAGGCCATCATC

TF

Transferring

GS106

-76

0.817

ACGGGAGGTCAAAGATTGCGCCC

ALDH2

aldehyde dehydrogenase 2 family (mitochondrial)

GS107

-332

0.817

CATTGGGGTCAAAGGCACACATT

APOC2

apolipoprotein C2

GS108

-159

0.916

TGTCTAGGCCAAAGTCCTGGCCA

PCK1

phosphoenolpyruvate carboxykinase 1 (soluble)

GS109

-455

0.923

GGTCACAGTCAAAGTTCATGGGA

NCOA2

nuclear receptor coactivator 2

GS110

-485

0.981

ATGGGAGGGCAAAGGGCAATGCC

TFF2

trefoil factor 2

GS111

-495

0.978

AAGATGGGACAAAGGGCATCGTG

CHEK1

CHK1 checkpoint homolog

GS112

+5

0.976

AGTGGTGGGCAAAGGACAGTCCG

CD63

CD63 antigen (melanoma 1 antigen)

GS113

-182

0.967

CTGCAGGAGCAAAGGACAGAAGT

SH3GL2

SH3-domain GRB2-like 2

GS114

-393

0.964

CGCCAGGCTCAAAGGGCAGGAGG

RND2

Rho family GTPase 2

GS115

 

0.923

AGGGCAGGTCAGAGTTCAAGCGA

ESRRBL1

estrogen-related receptor beta like 1

GS116

+63

0.91

CAGAACGGACAGAGTCCAGCGTG

DDB1

damage-specific DNA binding protein 1, 127 kDa

GS117

-295

0.909

GGGGAAGGGCAAAGGGCGCGGAA

NEUROG3

neurogenin 3

GS118

-225

0.896

GATTCCGGACAAAGGGCCGGGGT

IL6

interleukin-6

GS119

-149

0.889

ACTAGGGGGAAAAGTGCAGCTTA

AZI2

5-azacytidine induced 2

GS120

-217

0.793

GGACCCCCCAAAAGGACACTGAG

CFL2

cofilin 2 (muscle)

GS121

-676

0.792

CGAGGCGAGAAAAGCCCCCCGCA

GPHN

gephyrin

GS122

+733

0.79

GACTGAGAGGAAAGGATAGCACA

C14orf119

Chromosome 14 open reading frame 119

GS123

-610

0.786

CAAGCGGCTCAAAGGGGTGAGGA

PPP1R3C

protein phosphatase 1, regulatory (inhibitor) subunit 3C

GS124

-142

0.772

CGAGACGTGCAGAGAGCTATCTG

AKR1C3

aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)

GS125

-481

0.763

GAAAATGTAAAAAGGCAAATATT

NPAS2

neuronal PAS domain protein 2

GS126

-395

0.759

GAGCCGGCCCAGAGGAGAGGCAA

SAG

S-arrestin

GS127

-106

0.754

CCTGGGAGACAGAGCAAGACTCC

CLCN3

chloride channel 3

GS128

-377

0.753

AGCGTCACGCAGAGTTCGGATCC

CBX3

chromobox homolog 3 (HP1 gamma homolog, Drosophila)

GS129

-525

0.748

GCGGAAGGCTAGAGTCCTGCTAG

  1. *†The gene symbol and gene name of the gene where the corresponding HNF4 site was analyzed. ‡The internal name of the oligonucleotide used in the study. §Location of the site in the promoter of the gene. The position of the 5' end of the site is given relative to the TSS. The score was computed using the HNF4 PWM constructed in the course of this study (Table 2). ¥Sequence of the oligonucleotide used in the study. The central part of the oligonucleotide, which corresponds to the most conserved core of the HNF4 motif, is given in bold.
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Genome Biology

ISSN: 1474-760X

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