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Table 1 Summary of genes and analyses

From: A panel of genes methylated with high frequency in colorectal cancer

 

A

B

C

D

E

F

G

H

I

J

Gene

Down-regulated[32]

d-Aza/TSA activation

Bis-Tag tissue

Bis-Tag cells

SuBLiME

SuBLiME rank[16]

TCGA

Literature

Roche 454 sequencing

Tissue qMSP

ADAMTS1

Y

N

10

2

2

#

Y

[7, 21, 22, 24]

Y

 

ANK2

Y

Y

    

Y

  

Y

CA4

Y

Y

    

Y

[7]

 

Y

CFD

Y

N

       

Y

CHRDL1

Y

Y

    

Y

[7]

 

Y

COL1A2

Y

Y

10

2

4

699

Y

[7]

Y

 

COL4A1

Y

Y

  

2

1385

Y

[7, 24]

Y

Y

COL4A2

Y

Y

2

2

2

1608

Y

[7, 21]

Y

Y

CXCL12

Y

Y

    

Y

[7]

 

Y

EDIL3

Y

Y

10

2

4

#

Y

[7, 21]

Y

Y

EFEMP1

Y

Y

  

4

122

Y

[7, 18, 21]

Y

Y

EPB41L3

Y

Y

  

2

1217

 

[7]

 

Y

FBN1

Y

Y

10

2

4

705

Y

[7, 24, 26]

Y

 

FGFR2

Y

(+/-)

10

2

4

#

Y

 

Y

 

FOXF1

Y

N

10

2

4

82

Y

[7]

Y

Y

MAFB

Y

(+/-)

8

2

2

835

Y

[7, 24]

 

Y

MAMDC2

Y

Y

    

Y

  

Y

MEIS1

Y

Y

10

0

4

#

Y

[7]

Y

 

MMP2

Y

Y

10

4

2

446

Y

[7, 17, 18]

Y

 

MT1M

Y

N

     

[7]

 

Y

PPP1R14A

Y

Y

  

4

320

Y

[7, 21, 23]

Y

 

SCNN1B

Y

Y

    

Y

[18, 24]

 

Y

SDC2

Y

Y

10

4

4

300

Y

[7, 24]

Y

Y

TCF21

Y

Y

10

4

2

1420

Y

[7]

Y

 

ZSCAN18 (ZNF447)

Y

Y

  

4

245

 

[18, 20, 24]

 

Y

BCAT1

-

   

Y

137

Y

[7, 24]

 

Y

DLX5

-

 

Y

 

Y

249

Y

[23, 24]

Y

Y

FGF5

-

 

Y

    

[7, 17]

Y

Y

FOXB1

-

 

(Y)

 

Y

32

Y

 

Y

Y

FOXD2

-

 

Y

   

Y

[7, 18]

Y

 

FOXI2

-

   

Y

9

Y

[7]

 

Y

GRASP

-

 

(Y)

 

Y

76

Y

[7, 24]

Y

Y

IKZF1

-

   

Y

1

N

[7, 33]

 

Y

IRF4

-

   

Y

27

Y

[7, 18, 20, 24]

 

Y

IRX1

-

 

Y

 

Y

47

 

[7]

Y

Y

NPY

-

 

(Y)

 

Y

36

Y

[7, 17, 18, 24, 27]

Y

Y

PDX1

-

 

Y

   

Y

[7]

Y

Y

SEPT9

-

       

Y

Y

SLC6A15

-

 

Y

 

Y

1136

Y

[7, 18, 20, 24]

 

Y

SOX21

-

 

(Y)

 

Y

6

Y

[7]

Y

Y

ST8SIA1

-

   

Y

8

Y

[7]

 

Y

SUSD5

-

 

(Y)

 

Y

195

 

[7]

Y

 

ZNF471

-

 

Y

 

Y

18

Y

[7]

Y

Y

Controls

          

SEPT9

-

       

Y

Y

TMEFF2

-

      

[7, 17, 21, 24, 27]

Y

 
  1. Notes/Column.
  2. A. Down-regulated: designated ‘Y’ if gene was in list of differentially-expressed (down-regulated) genes identified in LaPointe et al., 2012 [32].
  3. B. D-AzaC/TSA activation; Genes with a 2-fold or greater change in gene expression ‘Y’, less than 2-fold ‘N’, borderline ‘(+/-)’.
  4. C. Bis-tag tissue: for genes initially recognised as down-regulated (rows 3-27), genes were scored for methylation difference between cancer and normal tissues on a scale of 0 to 10.
  5. For genes in rows 29-47, those designated ‘Y’ were among the top differentially methylated genes identified by Bis-tag (Additional file 2: Table S4). Those designated ‘(Y)’ were identified from SuBLiME data and differential methylation in clinical samples confirmed by inspection of Bis-tag plots.
  6. D. Bis-tag cells: for genes initially recognised as down-regulated (rows 3-27), genes were scored for methylation in CRC cell lines on a scale of 0 to 4.
  7. E. SuBLiME: for genes initially recognised as down-regulated (rows 3-27), genes were scored for methylation in CRC cell lines on a scale of 0 to 4. For genome-wide analysis (Rows 29-47), ‘Y’ indicates that gene was in list of differentially methylated genes (Ross et al. [16]).
  8. F. SuBLiME rank: shows ranking within list of differentially methylated genes.
  9. ‘#’ differential sites (Column E) for these genes were either not found in two or more cell lines or were located in regions outside the promoter region (-2 kb to + 1 kb of UCSC canonical transcription start site) surveyed in Ross et al. [16].
  10. G. TCGA: ‘Y’ denotes that differential methylation is confirmed in TCGA Illumina 27 K bead Chip data.
  11. H. Literature: references demonstrating methylation of gene in colorectal cancer.
  12. I. Roche 454 sequencing: ‘Y’ denotes included in multiplexed bisulfite sequencing.
  13. J. MSP on Tissues: ‘Y’ denotes include in MSP quantification of methylation levels in CRC tissue sample.
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BMC Cancer

ISSN: 1471-2407

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