Download Table S7-S8

Table S9. A. Cancer de novo methylated genes: GSC and GBM FFPE tissues vs. foetal NSCs.
The significant GO annotations related to the nervous system, development and differentiation
processes are listed. B. De novo aberrantly methylated genes in GSC lines. These genes are
exclusively de novo methylated in GSC lines compared with foetal NSC lines.
A. Cancer de novo methylated genes: GSC and GBM FFPE tissues vs. foetal NSCs.
Gene
BARHL2*
Chromosomal
location
1p22.2
Name
BarH-like homeobox 2
SIX2*
2p21
SIX homeobox 2
TBR1
2q24
T-box, brain, 1
GHSR
3q26.31
NKX3-2
PHOX2B*
4p16.3
4p12
TEC
PITX2*
MAB21L2
4p12
4q25
4q31
growth hormone
secretagogue receptor
NK3 homeobox 2
paired-like homeobox 2b
tec protein tyrosine kinase
paired-like homeodomain 2
mab-21-like 2 (C. elegans)
NEUROG1*
5q23-q31
neurogenin 1
ETV7*
TBX18*
HOXA9*
TBX20*
MOGAT3
6p21
6q14-q15
7p15.2
7p14.3
7q22.1
MIR183
PRDM14
DMRT2*
7q32.2
8q13.3
9p24.3
DMRT3*
9p24.3
FOXE1*
9q22
ets variant 7
T-box 18
homeobox A9
T-box 20
monoacylglycerol Oacyltransferase 3
microRNA 183
PR domain containing 14
doublesex and mab-3 related
transcription factor 2
doublesex and mab-3 related
transcription factor 3
forkhead box E1 (thyroid
transcription factor 2)
H6 family homeobox 2
goosecoid homeobox
aldehyde dehydrogenase 1
family, member A2
desmocollin 3
sal-like 3 (Drosophila)
NTPase, KAP family P-loop
domain containing 1
ESX homeobox 1
HMX2*
GSC*
ALDH1A2
10q26.13
14q32.1
15q21.3
DSC3
SALL3
NKPD1
18q12.1
18q23
19q13.32
ESX1
Xq22.1
Significant GO terms related to the
nervous system, development and
differentiation
cell fate determination; nervous system
development; neuron differentiation;
neuron migration
anatomical structure morphogenesis,
multicellular organism development
axon guidance; brain development;
hindbrain development
none
none
cell development; cell differentiation in
hindbrain; glial cell differentiation;
multicellular organism development;
nervous system development; neuron
migration; positive regulation of neuron
differentiation
none
multicellular organism development
multicellular organism development
nervous system development
cell fate commitment; multicellular
organism development; nervous system
development; neurogenesis; positive
regulation of neuron differentiation
none
multicellular organism development
none
none
none
none
cell fate specification; cell morphogenesis
none
cell differentiation; multicellular
organism development
none
none
multicellular organism development
none
none
none
none
none
B. De novo aberrantly methylated genes in GSC lines.
Gene
CACNA1E
ECEL1
Chromosomal
location
1q25-q31
2q37.1
RPL26L1
PTPRK
5q35.1
6q22.2-q22.3
TWIST1*
7p21.2
NEFL
8p21
SYT10
ISL2*
STAC2
12p11.1
15q23
17q12
SIM2*
21q22.13
Name
calcium channel, voltagedependent, R type, alpha 1E
subunit
endothelin converting
enzyme-like 1
ribosomal protein L26-like 1
protein tyrosine
phosphatase, receptor type,
K
twist homolog 1
(Drosophila)
neurofilament, light
polypeptide
synaptotagmin X
ISL LIM homeobox 2
SH3 and cysteine rich
domain 2
single-minded homolog 2
(Drosophila)
Significant GO terms related to the
nervous system, development and
differentiation
synaptic transmission
neuropeptide signaling pathway
none
none
anatomical structural development; cell
differentiation; multicellular organism
development
anterograde axon cargo transport; axon
transport of mitochondrion; intermediate
filament organization
neurofilament bundle assembly;
neurofilament bundle assembly;
retrograde axon cargo transport; synaptic
transmission
none
multicellular organism development
none
cell differentiation; embryonic pattern
specification; multicellular organism
development
*genes targeted by Suz12 in ES cells [1].
[1] Lee TI, Jenner RG, Boyer LA, Guenther MG, Levine SS, et al. (2006) Control of developmental
regulators by Polycomb in human embryonic stem cells. Cell 125: 301-313.