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Table 1 Examples of gene-expression changes in response to HDACi treatment or single class I HDAC enzyme depletion.

From: Differential effects of class I isoform histone deacetylase depletion and enzymatic inhibition by belinostat or valproic acid in HeLa cells

Gene symbol

Gene name

Probe nr.

Belinostat

Valproic acid

HDAC1 KD

HDAC2 KD

HDAC3 KD

Transcription

       

HDAC1

Histone deacetylase 1

201209_at

  

0.10

  

HDAC2

Histone deacetylase 2

201833_at

   

0.10

 

HDAC3

Histone deacetylase 3

216326_s_at

    

0.14

JUN

Jun oncogene (AP-1)

201465_s_at

  

0.38

0.41

0.42

SMAD3

SMAD family member 3

218284_at

  

0.53

0.49

0.55

RAF1

v-raf-1 murine leukemia viral oncogene homolog

201244_s_at

  

2.88

2.94

2.93

Metabolism

       

CTPS

CTP synthase

202613_at

0.39

0.44

   

TYMS

Thymidylate synthase

202589_at

0.62

0.43

   

FUCA

Fucosidase, alpha-L-1, tissue

202838_at

5.86

5.41

   

SAT1

Spermidine/spermine N1-acetyltransferase 1

210592_s_at

3.81

3.54

   

Cell cycle

       

CDKN1A

Cyclin-dependent kinase inhibitor 1A (p21, Cip1)

202284_s_at

4.15

3.16

   

CDC25B

Cell division cycle 25 homolog B

201853_s_at

0.68

0.58

   

HRASLS3

HRAS-like suppressor 3

209581_at

5.96

4.70

4.14

2.31

2.11

CCNB1

Cyclin B1

214710_s_at

0.55

0.39

   

CCND1

Cyclin D1

208712_at

0.38

    

CCND2

Cyclin D2

200951_s_at

 

2.29

   

CCNE1

Cyclin E1

213523_at

2.04

1.69

   

CCNG1

Cyclin G1

208796_s_at

  

4.39

4.11

3.31

Apoptosis

       

FAIM

Fas apoptotic inhibitory molecule

220643_s_at

0.32

0.17

   

BCL2L11

BCL2-like 11 (apoptosis facilitator) (BIM)

1555372_at

1.95

    

CASP3

Caspase 3

202763_at

   

0.51

0.52

CASP7

Caspase 7

207181_s_at

  

1.86

1.72

1.53

CASP9

Caspase 9

203984_s_at

  

1.57

3.24

1.87

FAS

FAS (TNF receptor superfamily, member 6)

216252_x_at

  

1.55

 

0.65

Cell signaling

       

RASGRP2

RAS guanyl releasing protein 2

214369_s_at

3.16

6.06

   

MYC

v-myc myelocytomatosis viral oncogene homolog

202431_s_at

0.43

    

MINA

MYC induced nuclear antigen

213189_at

0.31

0.40

   

TGFα

Transforming growth factor, alpha

205016_at

 

3.24

   

RASGRP1

RAS guanyl releasing protein 1

205590_at

  

0.12

0.10

0.25

CGA

glycoprotein hormones, alpha polypeptide

204637_at

5.30

4.36

2.66

16.53

6.27

Miscellaneous

       

KPNB1

Importin β

208975_s_at

0.67

0.57

   

SERPINE1

Serpin peptidase inhibitor, clade E

202627_s_at

  

0.21

0.23

0.22

EDN1

Endothelin 1

218995_s_at

  

0.45

0.45

0.45

THBS1

Thrombospondin 1

201108_s_at

  

0.30

0.30

0.51

ADAM19

ADAM metallopeptidase domain 19

209765_at

  

0.33

 

0.37

PDK4

Pyruvate dehydrogenase kinase 4

205960_at

4.13

7.34

2.74

3.31

4.38

ATP10D

ATPase, Class V, type 10D

213238_at

3.85

3.46

2.40

2.04

2.88

  1. Absolute fold-changes related to untreated or scrambled control for HDACi (VPA or belinostat) or HDAC 1, 2, or 3 KD samples respectively are listed. Blank fields correspond to no significant changes above 1.5-fold. The complete gene list of all genes regulated by 2-fold or more is accessible as supplementary material (Table A).
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Molecular Cancer

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