Table 2 |
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|
Transcripts where 97% of the variance in gene expression is explained by growth conditions |
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|
Affymetrix Probe IDa |
Gene Symbol |
Entrez GeneID |
Gene Description |
Growth Prop. of Varianceb |
F testc |
ρ0 Vivo/ρ0 Vitro |
WT Vivo/WT Vivo |
|||
|
FCd |
Pe |
FCd |
Pe |
|||||||
|
|
||||||||||
|
Up-regulated and dependent on growth conditions |
211571_s_at |
CSPG2 |
1462 |
chondroitin sulfate proteoglycan 2 |
0.99 |
1.41 × 10-12 |
34.6 |
0.0001 |
19.0 |
0.0002 |
|
215646_s_at |
CSPG2 |
1462 |
chondroitin sulfate proteoglycan 2 |
0.99 |
2.52 × 10-12 |
33.5 |
0.0003 |
20.3 |
0.0003 |
|
|
220952_s_at |
PLEKHA5 |
54477 |
PI 3-phosphate-binding protein-2 |
0.99 |
1.79 × 10-11 |
6.7 |
0.0003 |
5.6 |
0.0006 |
|
|
209090_s_at |
SH3GLB1 |
51100 |
SH3-domain GRB2-like endophilin B1 |
0.99 |
2.86 × 10-10 |
3.0 |
0.0015 |
3.1 |
0.0002 |
|
|
216405_at |
LGALS1 |
3956 |
lectin, galactoside-binding, soluble, 1 |
0.98 |
6.43 × 10-12 |
11.5 |
0.0007 |
14.4 |
0.0006 |
|
|
212254_s_at |
DST |
667 |
dystonin |
0.98 |
3.64 × 10-11 |
3.9 |
0.0006 |
4.7 |
0.0003 |
|
|
201056_at |
GOLGB1 |
2804 |
golgin B1, golgi integral mem. protein |
0.98 |
2.12 × 10-10 |
3.3 |
0.0008 |
2.9 |
0.0004 |
|
|
221829_s_at |
TNPO1 |
3842 |
transportin 1 |
0.98 |
2.86 × 10-10 |
4.0 |
0.0012 |
3.9 |
0.0005 |
|
|
204619_s_at |
CSPG2 |
1462 |
chondroitin sulfate proteoglycan 2 |
0.98 |
3.01 × 10-11 |
12.2 |
0.0003 |
7.5 |
0.0003 |
|
|
205173_x_at |
CD58 |
965 |
CD58 molecule |
0.98 |
1.70 × 10-10 |
3.5 |
0.0014 |
3.7 |
0.0004 |
|
|
218901_at |
PLSCR4 |
57088 |
phospholipid scramblase 4 |
0.98 |
1.32 × 10-9 |
3.5 |
0.0009 |
3.8 |
0.0014 |
|
|
213229_at |
DICER1 |
23405 |
Dicer1, Dcr-1 homolog |
0.97 |
2.18 × 10-10 |
6.1 |
0.0009 |
7.0 |
0.0013 |
|
|
208772_at |
ANKHD1 |
404734 |
ankyrin repeat & KH domain containing 1 |
0.97 |
1.97 × 10-9 |
2.5 |
0.0027 |
2.4 |
0.0003 |
|
|
221731_x_at |
CSPG2 |
1462 |
chondroitin sulfate proteoglycan 2 |
0.97 |
4.35 × 10-11 |
104.7 |
0.0001 |
30.9 |
0.0002 |
|
|
201057_s_at |
GOLGB1 |
2804 |
golgin B1, golgi integral mem. protein |
0.97 |
1.39 × 10-9 |
3.2 |
0.0027 |
2.9 |
0.0002 |
|
|
214295_at |
KIAA0485 |
57235 |
KIAA0485 protein |
0.97 |
4.14 × 10-10 |
3.9 |
0.0014 |
4.1 |
0.0008 |
|
|
201024_x_at |
EIF5B |
9669 |
eukaryotic translation initiation factor 5B |
0.97 |
2.66 × 10-9 |
2.3 |
0.0012 |
2.2 |
0.0012 |
|
|
201280_s_at |
DAB2 |
1601 |
disabled homolog 2 |
0.97 |
4.14 × 10-10 |
5.3 |
0.0004 |
3.5 |
0.0006 |
|
|
218396_at |
VPS13C |
54832 |
vacuolar protein sorting 13 homolog C |
0.97 |
8.54 × 10-10 |
4.4 |
0.0012 |
4.8 |
0.0006 |
|
|
205383_s_at |
ZBTB20 |
26137 |
zinc finger and BTB domain containing 20 |
0.97 |
5.52 × 10-10 |
4.2 |
0.0011 |
6.7 |
0.0003 |
|
|
219221_at |
ZBTB38 |
253461 |
zinc finger and BTB domain containing 38 |
0.97 |
2.98 × 10-12 |
6.0 |
0.0007 |
6.5 |
0.0003 |
|
|
208663_s_at |
TTC3 |
7267 |
tetratricopeptide repeat domain 3 |
0.97 |
1.19 × 10-9 |
3.1 |
0.0021 |
3.1 |
0.0013 |
|
|
212070_at |
GPR56 |
9289 |
G protein-coupled receptor 56 |
0.97 |
3.78 × 10-10 |
3.3 |
0.0007 |
4.3 |
0.0008 |
|
|
203216_s_at |
MYO6 |
4646 |
myosin VI |
0.97 |
2.35 × 10-9 |
3.1 |
0.0018 |
2.7 |
0.0012 |
|
|
204620_s_at |
CSPG2 |
1462 |
chondroitin sulfate proteoglycan 2 |
0.97 |
6.97 × 10-11 |
104.5 |
0.0001 |
27.8 |
0.0002 |
|
|
212062_at |
ATP9A |
10079 |
ATPase, Class II, type 9A |
0.97 |
2.73 × 10-9 |
2.5 |
0.0002 |
2.7 |
0.0030 |
|
|
213775_x_at |
ZNF638 |
27332 |
zinc finger protein 638 |
0.97 |
2.86 × 10-10 |
2.6 |
0.0008 |
3.0 |
0.0005 |
|
|
Down-regulated and dependent on growth conditions |
213201_s_at |
TNNT1 |
7138 |
troponin T type 1 |
0.99 |
6.43 × 10-12 |
-6.9 |
0.0002 |
-5.0 |
0.0003 |
|
212432_at |
GRPEL1 |
80273 |
GrpE-like 1, mitochondrial |
0.99 |
1.37 × 10-9 |
-2.3 |
0.0008 |
-2.3 |
0.0005 |
|
|
209507_at |
RPA3 |
6119 |
replication protein A3, 14 kDa |
0.98 |
6.76 × 10-10 |
-2.2 |
0.0010 |
-2.3 |
0.0002 |
|
|
209825_s_at |
UCK2 |
7371 |
uridine-cytidine kinase 2 |
0.98 |
1.09 × 10-9 |
-2.5 |
0.0019 |
-2.3 |
0.0006 |
|
|
202533_s_at |
DHFR |
1719 |
dihydrofolate reductase |
0.98 |
3.51 × 10-9 |
-2.1 |
0.0013 |
-2.0 |
0.0006 |
|
|
201577_at |
NME1 |
4830 |
non-metastatic cells 1, protein expressed |
0.97 |
2.29 × 10-9 |
-2.1 |
0.0014 |
-2.0 |
0.0004 |
|
|
208756_at |
EIF3S2 |
8668 |
euk. transl. init. factor 3, subunit 2 beta |
0.97 |
1.92 × 10-8 |
-1.8 |
0.0002 |
-1.7 |
0.0013 |
|
|
207239_s_at |
PCTK1 |
5127 |
PCTAIRE protein kinase 1 |
0.97 |
6.29 × 10-9 |
-1.9 |
0.0017 |
-1.9 |
0.0007 |
|
|
204126_s_at |
CDC45L |
8318 |
CDC45 cell division cycle 45-like |
0.97 |
2.31 × 10-8 |
-2.0 |
0.0030 |
-1.9 |
0.0004 |
|
|
219162_s_at |
MRPL11* |
65003 |
mitochondrial ribosomal protein L11 |
0.97 |
1.37 × 10-9 |
-2.5 |
0.0010 |
-2.2 |
0.0006 |
|
|
208847_s_at |
ADH5 |
128 |
alcohol dehydrogenase 5, chi polypeptide |
0.97 |
5.92 × 10-8 |
-1.7 |
0.0022 |
-1.6 |
0.0007 |
|
|
210250_x_at |
ADSL |
158 |
adenylosuccinate lyase |
0.97 |
4.04 × 10-9 |
-2.0 |
0.0015 |
-2.3 |
0.0012 |
|
|
208799_at |
PSMB5 |
5693 |
proteasome beta 5 subunit |
0.97 |
2.6 × 10-8 |
-1.9 |
0.0025 |
-1.8 |
0.0004 |
|
|
221620_s_at |
NOMO3 |
408050 |
NODAL modulator 3 |
0.97 |
1.64 × 10-9 |
-2.0 |
0.0015 |
-2.3 |
0.0004 |
|
|
210519_s_at |
NQO1 |
1728 |
NAD(P)H dehydrogenase, quinone 1 |
0.97 |
7.60 × 10-9 |
-2.1 |
0.0020 |
-1.8 |
0.0007 |
|
|
208910_s_at |
C1QBP |
708 |
splicing factor SF2-associated protein |
0.97 |
1.63 × 10-9 |
-2.4 |
0.0020 |
-2.5 |
0.0008 |
|
|
201903_at |
UQCRC1 |
7384 |
ubiquinol-cytochrome c reductase |
0.97 |
9.25 × 10-9 |
-1.8 |
0.0019 |
-2.1 |
0.0009 |
|
|
200039_s_at |
PSMB2 |
5690 |
proteasome subunit, beta type, 2 |
0.97 |
5.72 × 10-9 |
-1.9 |
0.0022 |
-2.0 |
0.0006 |
|
|
217960_s_at |
TOMM22 |
56993 |
mitochondrial import receptor Tom22 |
0.97 |
1.04 × 10-8 |
-2.2 |
0.0007 |
-1.9 |
0.0014 |
|
|
205691_at |
SYNGR3 |
9143 |
synaptogyrin 3 |
0.97 |
1.83 × 10-9 |
-3.1 |
0.0012 |
-2.4 |
0.0012 |
|
|
|
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|
aOnly probe tilings representing genes with annotated functions are provided bProportion of variance in gene expression due to growth conditions (i.e. cultured cells or xenografts) cBayes modified F test (multiple hypothesis corrected) dFold-change eBenjamini and Hochberg corrected two-tailed Student's t-test |
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|
Magda et al. BMC Genomics 2008 9:521 doi:10.1186/1471-2164-9-521 |
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