Table 1.
Summary of genes and analyses
| |
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 |
Notes/Column.
A. Down-regulated: designated ‘Y’ if gene was in list of differentially-expressed (down-regulated) genes identified in LaPointe et al., 2012 [32].
B. D-AzaC/TSA activation; Genes with a 2-fold or greater change in gene expression ‘Y’, less than 2-fold ‘N’, borderline ‘(+/-)’.
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.
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.
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.
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]).
F. SuBLiME rank: shows ranking within list of differentially methylated genes.
‘#’ 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].
G. TCGA: ‘Y’ denotes that differential methylation is confirmed in TCGA Illumina 27 K bead Chip data.
H. Literature: references demonstrating methylation of gene in colorectal cancer.
I. Roche 454 sequencing: ‘Y’ denotes included in multiplexed bisulfite sequencing.
J. MSP on Tissues: ‘Y’ denotes include in MSP quantification of methylation levels in CRC tissue sample.