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Table 1 Genes differentially expressed with RA in RIP140 siRNA treated NT2/D1 cells

From: Selective repression of retinoic acid target genes by RIP140 during induced tumor cell differentiation of pluripotent human embryonal carcinoma cells

Gene symbol

Gene description

RA fold-change in control siRNA cells

RA fold-change in RIP140 siRNA cells

Differential fold-change

p-value

HOXA5

Homeobox A5

+1.60

+20.66

+12.88

0.000368

TSHZ1

Teashirt family zinc finger 1

+2.15

+18.87

+8.76

0.001052

DMRT1

Doublesex and mab-3 related transcription factor 1

-1.09

+3.99

+4.35

0.010148

C8orf72

Chromosome 8 open reading frame 72

+2.34

+9.85

+4.21

0.022663

ZADH2

Zinc binding alcohol dehydrogenase, domain containing 2

+1.48

+5.67

+3.84

0.011172

VSNL1

Visinin-like 1

-3.89

-14.60

-3.75

0.000767

RARB

Retinoic acid receptor, beta

+7.99

+26.90

+3.37

0.012977

PYCR2

Pyrroline-5-carboxylate reductase family, member 2

+32.66

+104.63

+3.20

0.011152

DEPDC6

DEP domain containing 6

+2.76

+8.67

+3.15

0.026040

KCNJ4

Potassium inwardly-rectifying channel, subfamily J, member 4

+3.72

+11.52

+3.10

0.008146

HOXB5

Homeobox B5

+1.40

+4.19

+2.99

0.031222

MEIS1

Meis1, myeloid ecotropic viral integration site 1 homolog (mouse)

+3.09

+9.06

+2.93

0.022140

-

DKFZP686A01247 hypothetical protein

+1.92

+5.28

+2.76

0.006054

FLJ12624

Phospholipase A2 homolog

-3.20

-8.31

-2.59

0.000778

SUSD3

Sushi domain containing 3

+3.07

+7.89

+2.57

0.023342

EDG7

Endothelial differentiation, lysophosphatidic acid G-protein recept

-1.58

-4.02

-2.55

0.019311

NRP1

Neuropilin 1

+1.54

+3.84

+2.50

0.024092

KIF21B

Kinesin family member 21B

-1.04

+2.37

+2.46

0.001602

INHBB

Inhibin, beta B (activin AB beta polypeptide)

+1.22

+2.95

+2.42

0.001612

HOXB13

Homeobox B13

+1.21

+2.82

+2.34

0.028115

OVOS2

Ovostatin 2

-1.66

-3.85

-2.32

0.001967

HLA-DPB1

Major histocompatibility complex, class II, DP beta 1

-2.07

-4.79

-2.31

0.048107

EMILIN2

Elastin microfibril interfacer 2

-1.65

-3.72

-2.25

0.010781

HAS3

Hyaluronan synthase 3

-1.75

-3.86

-2.21

0.001436

NR6A1

Nuclear receptor subfamily 6, group A, member 1

-1.02

+2.17

+2.21

0.014380

ATBF1

AT motif binding factor 1

+2.93

+6.45

+2.20

0.000101

NODAL

Nodal homolog (mouse)

+1.20

+2.60

+2.16

0.001068

ZNF703

Zinc finger protein 703

+2.62

+5.67

+2.16

0.046510

PCDH17

Protocadherin 17

+2.71

+5.81

+2.14

0.046724

PAPPA

Pregnancy-associated plasma protein A, pappalysin 1

+1.43

-1.48

-2.11

0.026579

KLHL7

Kelch-like 7 (Drosophila)

-1.34

-2.81

-2.09

0.039448

LNX1

Ligand of numb-protein × 1

-1.13

-2.30

-2.04

0.008236

PRKCH

Protein kinase C, eta

+1.99

+4.05

+2.04

0.036242

TBX3

T-box 3 (ulnar mammary syndrome)

+4.45

+9.01

+2.03

0.046092

ADM

Adrenomedullin

-1.15

-2.32

-2.02

0.019731

KCTD12

Potassium channel tetramerisation domain containing 12

-1.03

-2.08

-2.02

0.003013

PTPRU

Protein tyrosine phosphatase, receptor type, U

+1.16

+2.32

+1.99

0.006395

WNT3

Wingless-type MMTV integration site family, member 3

+3.05

+1.53

-1.99

0.009256

MCOLN3

Mucolipin 3

-1.26

-2.48

-1.97

0.041576

PCAF

P300/CBP-associated factor

+1.64

+3.22

+1.97

0.017906

LOC645323

Hypothetical LOC645323

+6.84

+13.40

+1.96

0.002997

EPAS1

Endothelial PAS domain protein 1

+1.01

-1.93

-1.96

0.007540

WDR68

WD repeat domain 68

+1.07

+2.09

+1.96

0.000433

CNR1

Cannabinoid receptor 1 (brain)

+11.84

+23.16

+1.96

0.006641

FAM46B

Family with sequence similarity 46, member B

-3.48

-6.81

-1.95

0.015572

FOXD3

Forkhead box D3

-3.72

-7.26

-1.95

0.018665

PPFIBP2

PTPRF interacting protein, binding protein 2 (liprin beta 2)

-1.17

-2.25

-1.92

0.001765

AK3L1

Adenylate kinase 3-like 1

-4.02

-7.69

-1.91

0.001875

MAP3K5

Mitogen-activated protein kinase kinase kinase 5

-1.12

+1.70

+1.90

0.020647

  1. Gene list represents genes in scatter plot of Figure 3D; Group 4 (siRNA RIP140 RA) vs. Group 2 (control siRNA RA). Genes with a p-value < 0.05 are ranked by fold change between the expression of Group 4 vs. Group 2 (Differential fold change). Values corresponding to scatter plot of Figure 3A, Group 2 vs. Group 1 (RA-fold change in control siRNA cells) and scatter plot of Figure 3C, Group 4 vs. Group 3 (RA-fold change in RIP140 siRNA cells) are also provided. For genes with multiple probe sets, the probe set with the greatest differential expression was chosen. In bold are the two genes where RIP140 siRNA lessens the extent or direction of RA-mediated regulation.
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