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Table 2 Examples of differentially expressed genes.

From: Silencing of core transcription factors in human EC cells highlights the importance of autocrine FGF signaling for self-renewal

  

hEC cells

hES cells

 

Symbol

Gene Name

Ratio RNAi/mock

ChIP-chip data [8]

Ratio

down-regulated genes

OCT4

NANOG

SOX2

OCT4

NANOG

SOX2

hES/uni

DPPA4

developmental pluripotency associated 4

0.1

0.4

0.1

+

+

+

5

ERBB2

v-erb-b2 erythroblastic leukemia viral oncogene homolog 2

0.6

2.1

0.4

-

+

+

8

FEZ1

fasciculation and elongation protein zeta 1

0.1

3.2

0.1

+

+

+

6

FLJ10884

hypothetical protein FLJ10884

0.3

0.8

0.3

-

+

+

17

FOXO1A

forkhead box O1A

0.5

1.1

0.5

+

+

+

9

GDF3

growth differentiation factor 3

0.0

0.4

0.0

-

+

-

 

HESX1

homeo box 1

0.2

0.2

0.2

+

+

+

5

H2AFX

H2A histone family, member X

0.6

1.0

0.6

-

+

+

 

HIST1H2BE

histone 1, H2be

0.6

1.0

0.6

+

+

+

 

HIST1H2BG

histone 1, H2bg

0.6

0.7

0.5

-

+

+

 

HIST1H2BH

histone 1, H2bh

0.5

0.9

0.5

-

+

+

 

HIST1H2BJ

histone 1, H2bj

0.4

0.9

0.4

-

-

+

 

HIST1H3D

histone 1, H3d

0.4

0.8

0.4

+

+

+

 

HIST1H3F

histone 1, H3f

0.4

0.7

0.4

-

+

+

 

HIST1H3J

histone 1, H3j

0.5

0.6

0.5

+

+

+

 

HIST2H2AC

histone 2, H2ac

0.6

1.0

0.6

+

-

+

 

HIST2H2BE

histone 2, H2be

0.5

0.7

0.5

+

-

+

 

HIST2H3C

histone 2, H3c

0.2

0.6

0.2

-

+

+

 

HIST2H4

histone 2, H4

0.3

0.7

0.3

+

+

+

 

HIST3H2A

histone 3, H2a

0.3

1.0

0.3

-

+

+

 

NANOG

Nanog homeobox

0.1

0.2

0.1

+

+

+

24

POU5F1

POU domain, class 5, transcription factor 1

0.0

0.7

0.0

+

+

+

24

PRDM14

PR domain containing 14

0.2

0.3

0.2

+

+

+

15

SMARCA3

SWI/SNF related [...] regulator of chromatin [...]

0.5

0.5

0.5

-

+

+

 

STAT3

signal transducer and activator of transcription 3

0.6

1.5

0.6

+

+

+

 

TDGF1

teratocarcinoma-derived growth factor 1

0.1

0.7

0.1

+

+

+

41

TERF1

telomeric repeat binding factor 1

0.2

0.3

0.2

-

+

-

18

TRIM22

tripartite motif-containing 22

0.3

1.3

0.3

+

+

+

5

ZIC2

Zic family member 2

0.4

0.5

0.4

+

+

+

5

ZIC3

Zic family member 3 heterotaxy 1

0.3

1.0

0.3

+

+

+

8

ZNF206

zinc finger protein 206

0.0

0.3

0.0

-

+

-

43

AASS

aminoadipate-semialdehyde synthase

0.6

0.8

0.5

   

12

DNMT3B

DNA-methyltransferase 3 beta

0.2

0.6

0.2

   

21

DPPA3

developmental pluripotency associated 3 (STELLA)

0.1

0.7

0.0

    

KLF4

Kruppel-like factor 4

0.2

0.8

0.2

    

LIN28

lin-28 homolog

0.6

1.0

0.7

   

9

MYST2

MYST histone acetyltransferase 2

0.3

0.6

0.3

   

4

SOX13

SRY-box 13

0.4

1.1

0.4

   

4

SOX8

SRY-box 8

0.2

0.9

0.2

   

5

THY1

Thy-1 cell surface antigen

0.2

0.3

0.1

   

6

UTF1

undifferentiated embryonic cell transcription factor 1

0.1

0.5

0.0

   

26

ZNF589

zinc finger protein 589

0.5

1.0

0.5

   

7

up-regulated genes

BMP7

bone morphogenetic protein 7

2.7

0.9

3.0

+

+

+

 

LEFTA

left-right determination, factor A

50.6

6.6

54.6

+

+

+

4

HAND1

heart and neural crest derivatives expressed 1

9.1

3.8

8.1

+

+

+

 

HDAC9

histone deacetylase 9, transcript variant 3

2.3

1.0

2.1

-

-

+

 

JUN

v-jun sarcoma virus 17 oncogene homolog

7.6

2.0

9.4

-

+

-

 

KRT18

keratin 18

2.9

0.5

3.0

-

+

-

 

MEIS2

Meis1, myeloid ecotropic viral integration site 1 homolog 2

2.5

2.1

2.8

+

-

-

 

ATBF1

AT-binding transcription factor 1

2.2

2.3

2.3

+

+

+

 

DLX1

distal-less homeo box 1

4.1

1.0

4.0

+

+

+

 

DLX2

distal-less homeo box 2

9.3

1.3

9.1

+

-

-

 

ISL1

ISL1 transcription factor, LIM/homeodomain

9.0

0.7

7.2

+

+

+

 

LHX1

LIM homeobox 1

2.0

1.0

1.5

+

+

-

 

LHX2

LIM homeobox 2

5.8

0.9

6.2

+

+

+

 

LHX5

LIM homeobox 5

2.9

1.0

1.7

+

+

+

 

PHTF2

putative homeodomain transcription factor 2

1.7

1.3

1.8

-

+

-

 

ZFHX1B

zinc finger homeobox 1b

1.8

1.8

2.2

+

+

+

 

DLX3

distal-less homeo box 3

3.1

1.3

2.9

    

IRX3

iroquois homeobox protein 3

4.0

1.0

3.7

    

IRX4

iroquois homeobox protein 4

2.5

1.0

2.6

   

4

MSX1

msh homeo box homolog 1

4.9

1.0

4.8

    

MSX2

msh homeo box homolog 2

1.6

0.6

1.6

    

PKNOX2

PBX/knotted 1 homeobox 2

4.9

2.5

5.9

    

PRRX2

paired related homeobox 2

1.9

1.8

1.8

    

ZHX1

zinc fingers and homeoboxes 1

3.1

1.0

3.3

    
  1. Ratios > 1.5 or < 0.67 are in bold. In essentially all cases, these changes were also statistically significant. hESC ChIP-chip data were taken from [8]. The last column (expression ratio > 3 of H9 hES cells vs. universal reference RNA) indicates enriched gene expression in hES cells. SOX2 was below detection on the arrays but monitored by real-time PCR (Fig. 1A). See Additional file 5 for additional confirmations.
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BMC Developmental Biology

ISSN: 1471-213X

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