Table 2. Differentially expressed genes from the “Cell Cycle, Mitotic” FGS.
| DU-145 | PC3 | |||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| |
|
|
SAHA |
VPA |
SAHA |
VPA |
||||||||||||
| |
|
|
48 h |
96 h |
48 h |
96 h |
48 h |
96 h |
48 h |
96 h |
||||||||
| SYMBOL |
GENENAME |
ENTREZID |
Log2 Fold Change |
FDR |
Log2 Fold Change |
FDR |
Log2 Fold Change |
FDR |
Log2 Fold Change |
FDR |
Log2 Fold Change |
FDR |
Log2 Fold Change |
FDR |
Log2 Fold Change |
FDR |
Log2 Fold Change |
FDR |
| ACTR1A |
ARP1 actin-related protein 1 homolog A, centractin α (yeast) |
10121 |
– |
– |
– |
– |
– |
– |
– |
– |
0.36 |
0.000540 |
0.39 |
0.000235 |
– |
– |
– |
– |
| ANAPC1 |
anaphase promoting complex subunit 1 |
64682 |
-0.59 |
0.000293 |
-0.73 |
0.000042 |
-0.57 |
0.000263 |
-0.58 |
0.000180 |
– |
– |
– |
– |
– |
– |
– |
– |
| AURKA |
aurora kinase A |
6790 |
-0.74 |
0.000005 |
-0.87 |
0.000001 |
-0.60 |
0.000013 |
-0.70 |
0.000003 |
– |
– |
– |
– |
– |
– |
– |
– |
| AURKB |
aurora kinase B |
9212 |
– |
– |
– |
– |
-0.37 |
0.000118 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| BIRC5 |
baculoviral IAP repeat containing 5 |
332 |
-0.67 |
0.000294 |
-0.84 |
0.000039 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| BUB1 |
budding uninhibited by benzimidazoles 1 homolog (yeast) |
699 |
-0.70 |
0.000009 |
-0.65 |
0.000009 |
-0.47 |
0.000108 |
-0.64 |
0.000007 |
– |
– |
– |
– |
– |
– |
– |
– |
| BUB1B |
budding uninhibited by benzimidazoles 1 homolog β (yeast) |
701 |
-0.41 |
0.000125 |
-0.41 |
0.000088 |
-0.41 |
0.000084 |
-0.52 |
0.000011 |
– |
– |
– |
– |
– |
– |
– |
– |
| CCDC99 |
coiled-coil domain containing 99 |
54908 |
– |
– |
-0.30 |
0.000246 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| CCNA1 |
cyclin A1 |
8900 |
– |
– |
– |
– |
0.56 |
0.000001 |
0.54 |
0.000001 |
– |
– |
– |
– |
– |
– |
– |
– |
| CCNA2 |
cyclin A2 |
890 |
-0.58 |
0.000020 |
-0.56 |
0.000016 |
-0.62 |
0.000002 |
-0.70 |
0.000001 |
– |
– |
– |
– |
– |
– |
-0.36 |
0.000277 |
| CCNB1 |
cyclin B1 |
891 |
-0.85 |
0.000295 |
– |
– |
– |
– |
-0.82 |
0.000227 |
– |
– |
– |
– |
– |
– |
– |
– |
| CCNB2 |
cyclin B2 |
9133 |
-0.75 |
0.000028 |
-0.88 |
0.000006 |
– |
– |
-0.54 |
0.000165 |
– |
– |
– |
– |
– |
– |
– |
– |
| CCND1 |
cyclin D1 |
595 |
0.88 |
0.000053 |
0.93 |
0.000024 |
– |
– |
0.74 |
0.000095 |
– |
– |
– |
– |
– |
– |
– |
– |
| CCNE1 |
cyclin E1 |
898 |
– |
– |
1.24 |
0.000091 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| CDC20 |
cell division cycle 20 homolog (S. cerevisiae) |
991 |
-0.82 |
0.000002 |
-0.87 |
0.000001 |
-0.63 |
0.000007 |
-0.54 |
0.000018 |
– |
– |
– |
– |
– |
– |
– |
– |
| CDC25B |
cell division cycle 25 homolog B (S. pombe) |
994 |
– |
– |
-0.44 |
0.000121 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| CDC45 |
cell division cycle 45 homolog (S. cerevisiae) |
8318 |
-0.84 |
0.000010 |
-0.90 |
0.000003 |
-0.79 |
0.000008 |
-0.77 |
0.000007 |
– |
– |
– |
– |
– |
– |
– |
– |
| CDCA8 |
cell division cycle associated 8 |
55143 |
-0.78 |
0.000027 |
-0.86 |
0.000008 |
-0.65 |
0.000071 |
-0.66 |
0.000047 |
– |
– |
– |
– |
– |
– |
– |
– |
| CDK5RAP2 |
CDK5 regulatory subunit associated protein 2 |
55755 |
-0.35 |
0.000159 |
-0.41 |
0.000033 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| CDKN1A |
cyclin-dependent kinase inhibitor 1A (p21, Cip1) |
1026 |
– |
– |
1.80 |
0.000033 |
– |
– |
1.36 |
0.000220 |
– |
– |
– |
– |
– |
– |
– |
– |
| CDKN2D |
cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4) |
1032 |
– |
– |
– |
– |
0.81 |
0.000068 |
1.00 |
0.000010 |
– |
– |
0.69 |
0.000429 |
0.99 |
0.000039 |
1.18 |
0.000009 |
| CENPA |
centromere protein A |
1058 |
-0.62 |
0.000132 |
-0.70 |
0.000036 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| CENPF |
centromere protein F, 350/400kDa (mitosin) |
1063 |
– |
– |
-1.10 |
0.000029 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| CENPH |
centromere protein H |
64946 |
-0.66 |
0.000301 |
-0.87 |
0.000029 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| CENPM |
centromere protein M |
79019 |
-0.86 |
0.000002 |
-0.75 |
0.000003 |
-0.71 |
0.000005 |
-0.64 |
0.000006 |
-0.48 |
0.000223 |
– |
– |
– |
– |
– |
– |
| CENPN |
centromere protein N |
55839 |
-0.96 |
0.000013 |
-1.06 |
0.000004 |
-0.67 |
0.000129 |
-0.84 |
0.000016 |
– |
– |
– |
– |
– |
– |
– |
– |
| CEP41 |
centrosomal protein 41kDa |
95681 |
– |
– |
– |
– |
0.38 |
0.000027 |
0.34 |
0.000041 |
– |
– |
– |
– |
– |
– |
– |
– |
| CEP72 |
centrosomal protein 72kDa |
55722 |
– |
– |
-0.39 |
0.000138 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| CETN2 |
centrin, EF-hand protein, 2 |
1069 |
– |
– |
0.60 |
0.000195 |
– |
– |
– |
– |
– |
– |
0.62 |
0.000244 |
– |
– |
– |
– |
| CKS1B |
CDC28 protein kinase regulatory subunit 1B |
1163 |
-0.97 |
0.000084 |
-1.17 |
0.000014 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| DBF4 |
DBF4 homolog (S. cerevisiae) |
10926 |
-0.49 |
0.000063 |
-0.66 |
0.000007 |
– |
– |
-0.52 |
0.000018 |
– |
– |
– |
– |
– |
– |
– |
– |
| DHFR |
dihydrofolate reductase |
1719 |
-0.30 |
0.000275 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| DYNC1H1 |
dynein, cytoplasmic 1, heavy chain 1 |
1778 |
0.62 |
0.000004 |
0.55 |
0.000006 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| E2F1 |
E2F transcription factor 1 |
1869 |
-0.52 |
0.000238 |
-0.51 |
0.000201 |
-0.54 |
0.000128 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| FGFR1OP |
FGFR1 oncogene partner |
11116 |
-0.64 |
0.000048 |
-0.60 |
0.000049 |
-0.51 |
0.000170 |
-0.50 |
0.000151 |
– |
– |
– |
– |
– |
– |
– |
– |
| HAUS2 |
HAUS augmin-like complex, subunit 2 |
55142 |
– |
– |
– |
– |
– |
– |
-0.62 |
0.000030 |
– |
– |
– |
– |
– |
– |
– |
– |
| KIF20A |
kinesin family member 20A |
10112 |
-0.64 |
0.000006 |
-0.62 |
0.000005 |
-0.58 |
0.000008 |
-0.67 |
0.000002 |
– |
– |
– |
– |
– |
– |
– |
– |
| KIF23 |
kinesin family member 23 |
9493 |
– |
– |
-0.91 |
0.000046 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| LIG1 |
ligase I, DNA, ATP-dependent |
3978 |
-0.60 |
0.000004 |
-0.59 |
0.000003 |
-0.40 |
0.000041 |
-0.34 |
0.000125 |
– |
– |
– |
– |
– |
– |
– |
– |
| MAD2L1 |
MAD2 mitotic arrest deficient-like 1 (yeast) |
4085 |
– |
– |
-0.82 |
0.000086 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| MCM5 |
minichromosome maintenance complex component 5 |
4174 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
-0.51 |
0.000412 |
– |
– |
| MCM7 |
minichromosome maintenance complex component 7 |
4176 |
-0.55 |
0.000239 |
-0.60 |
0.000087 |
-0.70 |
0.000024 |
-0.61 |
0.000054 |
– |
– |
– |
– |
-0.51 |
0.000614 |
– |
– |
| MNAT1 |
menage a trois homolog 1, cyclin H assembly factor (Xenopus laevis) |
4331 |
0.34 |
0.000106 |
0.28 |
0.000304 |
0.43 |
0.000011 |
– |
– |
0.30 |
0.000370 |
– |
– |
0.46 |
0.000017 |
– |
– |
| NDC80 |
NDC80 kinetochore complex component homolog (S. cerevisiae) |
10403 |
-0.81 |
0.000021 |
-0.80 |
0.000015 |
– |
– |
-0.59 |
0.000112 |
– |
– |
– |
– |
– |
– |
– |
– |
| NDE1 |
nudE nuclear distribution E homolog 1 (A. nidulans) |
54820 |
– |
– |
-0.42 |
0.000050 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| NEK2 |
NIMA (never in mitosis gene a)-related kinase 2 |
4751 |
-0.36 |
0.000132 |
-0.33 |
0.000188 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| NSL1 |
NSL1, MIND kinetochore complex component, homolog (S. cerevisiae) |
25936 |
– |
– |
0.47 |
0.000175 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| NUF2 |
NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae) |
83540 |
-0.78 |
0.000002 |
-0.80 |
0.000001 |
– |
– |
-0.50 |
0.000027 |
– |
– |
– |
– |
– |
– |
– |
– |
| NUP133 |
nucleoporin 133kDa |
55746 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
-0.59 |
0.000444 |
– |
– |
| NUP160 |
nucleoporin 160kDa |
23279 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
-0.35 |
0.000069 |
| NUP37 |
nucleoporin 37kDa |
79023 |
– |
– |
-0.60 |
0.000042 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| NUP85 |
nucleoporin 85kDa |
79902 |
– |
– |
-0.44 |
0.000063 |
– |
– |
-0.40 |
0.000090 |
– |
– |
– |
– |
– |
– |
– |
– |
| ORC3 |
origin recognition complex, subunit 3 |
23595 |
-0.41 |
0.000029 |
-0.56 |
0.000002 |
-0.33 |
0.000095 |
-0.43 |
0.000010 |
– |
– |
– |
– |
– |
– |
– |
– |
| ORC6 |
origin recognition complex, subunit 6 |
23594 |
-0.69 |
0.000014 |
-0.55 |
0.000050 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| PAFAH1B1 |
platelet-activating factor acetylhydrolase 1b, regulatory subunit 1 (45kDa) |
5048 |
-0.50 |
0.000266 |
-0.59 |
0.000049 |
-0.66 |
0.000021 |
-0.84 |
0.000002 |
– |
– |
– |
– |
– |
– |
– |
– |
| PER2 |
period homolog 2 (Drosophila) |
8864 |
– |
– |
– |
– |
– |
– |
– |
– |
-0.75 |
0.000033 |
-0.72 |
0.000035 |
– |
– |
– |
– |
| PKMYT1 |
protein kinase, membrane associated tyrosine/threonine 1 |
9088 |
-0.56 |
0.000106 |
– |
– |
-0.50 |
0.000172 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| PLK4 |
polo-like kinase 4 |
10733 |
– |
– |
– |
– |
– |
– |
-0.55 |
0.000078 |
– |
– |
– |
– |
– |
– |
– |
– |
| PMF1 |
polyamine-modulated factor 1 |
11243 |
-0.44 |
0.000063 |
-0.43 |
0.000048 |
-0.55 |
0.000007 |
-0.59 |
0.000003 |
-0.40 |
0.000179 |
-0.40 |
0.000149 |
-0.36 |
0.000454 |
-0.40 |
0.000170 |
| POLE |
polymerase (DNA directed), epsilon |
5426 |
-0.24 |
0.000280 |
-0.28 |
0.000055 |
-0.26 |
0.000088 |
-0.26 |
0.000084 |
– |
– |
– |
– |
– |
– |
– |
– |
| PRIM2 |
primase, DNA, polypeptide 2 (58kDa) |
5558 |
– |
– |
0.46 |
0.000272 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| PRKAR2B |
protein kinase, cAMP-dependent, regulatory, type II, β |
5577 |
– |
– |
0.57 |
0.000191 |
0.93 |
0.000005 |
0.94 |
0.000003 |
– |
– |
– |
– |
– |
– |
– |
– |
| PSMB10 |
proteasome (prosome, macropain) subunit, β type, 10 |
5699 |
-0.88 |
0.000368 |
-0.93 |
0.000171 |
– |
– |
-1.02 |
0.000061 |
– |
– |
– |
– |
– |
– |
– |
– |
| PSMC1 |
proteasome (prosome, macropain) 26S subunit, ATPase, 1 |
5700 |
– |
– |
-0.71 |
0.000221 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| PSMC2 |
proteasome (prosome, macropain) 26S subunit, ATPase, 2 |
5701 |
– |
– |
– |
– |
-0.31 |
0.000257 |
-0.43 |
0.000014 |
– |
– |
– |
– |
– |
– |
– |
– |
| PSMC6 |
proteasome (prosome, macropain) 26S subunit, ATPase, 6 |
5706 |
– |
– |
– |
– |
– |
– |
-0.45 |
0.000076 |
– |
– |
– |
– |
– |
– |
– |
– |
| PSMD14 |
proteasome (prosome, macropain) 26S subunit, non-ATPase, 14 |
10213 |
– |
– |
-0.33 |
0.000083 |
– |
– |
-0.31 |
0.000097 |
– |
– |
– |
– |
– |
– |
– |
– |
| PSMD2 |
proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 |
5708 |
– |
– |
1.02 |
0.000028 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| PTTG1 |
pituitary tumor-transforming 1 |
9232 |
-0.64 |
0.000264 |
-0.80 |
0.000035 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| RAD21 |
RAD21 homolog (S. pombe) |
5885 |
-0.37 |
0.000336 |
-0.38 |
0.000199 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| RPA2 |
replication protein A2, 32kDa |
6118 |
-0.44 |
0.000217 |
-0.52 |
0.000046 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| SEH1L |
SEH1-like (S. cerevisiae) |
81929 |
-0.69 |
0.000006 |
-0.64 |
0.000006 |
-0.70 |
0.000003 |
-0.70 |
0.000002 |
-0.68 |
0.000008 |
-0.63 |
0.000014 |
-0.86 |
0.000003 |
-0.86 |
0.000002 |
| SGOL2 |
shugoshin-like 2 (S. pombe) |
151246 |
– |
– |
-0.39 |
0.000175 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| SKP2 |
S-phase kinase-associated protein 2, E3 ubiquitin protein ligase |
6502 |
-0.34 |
0.000178 |
-0.32 |
0.000171 |
-0.45 |
0.000015 |
-0.45 |
0.000010 |
– |
– |
– |
– |
– |
– |
– |
– |
| SPC25 |
SPC25, NDC80 kinetochore complex component, homolog (S. cerevisiae) |
57405 |
-0.62 |
0.000155 |
– |
– |
– |
– |
-0.56 |
0.000172 |
– |
– |
– |
– |
– |
– |
– |
– |
| TUBB |
tubulin, β class I |
203068 |
– |
– |
-0.63 |
0.000191 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| TUBB4A |
tubulin, β 4A class IVa |
10382 |
-0.55 |
0.000235 |
-0.62 |
0.000069 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| TUBB4B |
tubulin, β 4B class IVb |
10383 |
-0.47 |
0.000010 |
-0.44 |
0.000010 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| TUBGCP4 |
tubulin, gamma complex associated protein 4 |
27229 |
-0.35 |
0.000151 |
-0.39 |
0.000049 |
-0.41 |
0.000033 |
-0.50 |
0.000005 |
– |
– |
-0.30 |
0.000537 |
– |
– |
– |
– |
| TYMS |
thymidylate synthetase |
7298 |
-1.16 |
0.000001 |
-1.22 |
0.000001 |
-0.90 |
0.000004 |
-0.92 |
0.000002 |
– |
– |
– |
– |
– |
– |
– |
– |
| UBE2C |
ubiquitin-conjugating enzyme E2C |
11065 |
-0.45 |
0.000256 |
-0.59 |
0.000055 |
– |
– |
– |
– |
– |
– |
0.43 |
0.000178 |
– |
– |
– |
– |
| ZWINT | ZW10 interactor | 11130 | – | – | -0.45 | 0.000216 | – | – | – | – | – | – | – | – | – | – | – | – |
Table displaying genes from the “Cell Cycle, Mitotic” FGS (Pathway Commons Reactome database) that were significantly differentially expressed (Log-odds > 3, FDR < 0.007) in DU-145 and PC3 cell lines upon HDACi-treatment with VPA or vorinostat (SAHA). In DU-145 cells most gene changes involved a downregulation of the genes; in PC3 cells only few genes proved to be differentially expressed and less FGS related to mitosis were altered. P-values per gene can be found in the Supplemental Material and at http://luigimarchionni.org/HDACIs.html.