Table 1. Differentially expressed genes from the “Signaling in Immune system” 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 |
| B2M |
β-2-microglobulin |
567 |
0.74 |
0.000021 |
0.80 |
0.000007 |
0.96 |
0.000002 |
0.92 |
0.000002 |
0.61 |
0.000138 |
0.68 |
0.000046 |
0.60 |
0.000172 |
0.56 |
0.000217 |
| C3 |
complement component 3 |
718 |
1.19 |
0.000025 |
– |
– |
1.12 |
0.000025 |
0.85 |
0.000165 |
– |
– |
– |
– |
– |
– |
– |
– |
| CD44 |
CD44 molecule (Indian blood group) |
960 |
0.76 |
0.000151 |
0.74 |
0.000125 |
– |
– |
– |
– |
– |
– |
– |
– |
-0.78 |
0.000211 |
– |
– |
| CDH1 |
cadherin 1, type 1, E-cadherin (epithelial) |
999 |
– |
– |
– |
– |
1.07 |
0.000007 |
1.24 |
0.000002 |
– |
– |
– |
– |
– |
– |
– |
– |
| CFD |
complement factor D (adipsin) |
1675 |
– |
– |
– |
– |
0.54 |
0.000005 |
0.45 |
0.000013 |
– |
– |
– |
– |
– |
– |
– |
– |
| CSF2 |
colony stimulating factor 2 (granulocyte-macrophage) |
1437 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
0.96 |
0.000588 |
| DDX58 |
DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 |
23586 |
– |
– |
– |
– |
– |
– |
0.63 |
0.000172 |
– |
– |
0.69 |
0.000193 |
– |
– |
– |
– |
| EGR1 |
early growth response 1 |
1958 |
– |
– |
– |
– |
– |
– |
1.68 |
0.000011 |
– |
– |
– |
– |
– |
– |
– |
– |
| FYN |
FYN oncogene related to SRC, FGR, YES |
2534 |
– |
– |
– |
– |
0.67 |
0.000022 |
0.78 |
0.000004 |
– |
– |
– |
– |
– |
– |
0.51 |
0.000334 |
| GAB2 |
GRB2-associated binding protein 2 |
9846 |
– |
– |
– |
– |
– |
– |
0.43 |
0.000148 |
– |
– |
– |
– |
– |
– |
0.42 |
0.000398 |
| GBP2 |
guanylate binding protein 2, interferon-inducible |
2634 |
– |
– |
– |
– |
0.52 |
0.000019 |
0.64 |
0.000003 |
– |
– |
– |
– |
– |
– |
– |
– |
| HLA-A |
major histocompatibility complex, class I, A |
3105 |
0.71 |
0.000221 |
0.66 |
0.000263 |
1.01 |
0.000010 |
1.23 |
0.000002 |
0.67 |
0.000533 |
– |
– |
– |
– |
0.69 |
0.000365 |
| HLA-B |
major histocompatibility complex, class I, B |
3106 |
0.85 |
0.000105 |
0.90 |
0.000046 |
0.69 |
0.000043 |
1.01 |
0.000002 |
0.90 |
0.000115 |
0.71 |
0.000069 |
– |
– |
0.94 |
0.000065 |
| HLA-C |
major histocompatibility complex, class I, C |
3107 |
0.88 |
0.000010 |
0.98 |
0.000003 |
1.02 |
0.000002 |
1.33 |
0.000000 |
0.82 |
0.000022 |
0.92 |
0.000008 |
0.78 |
0.000034 |
1.09 |
0.000003 |
| HLA-F |
major histocompatibility complex, class I, F |
3134 |
0.57 |
0.000295 |
0.62 |
0.000121 |
0.85 |
0.000010 |
1.13 |
0.000001 |
0.61 |
0.000294 |
0.66 |
0.000135 |
– |
– |
0.73 |
0.000065 |
| HLA-G |
major histocompatibility complex, class I, G |
3135 |
– |
– |
– |
– |
0.81 |
0.000243 |
1.19 |
0.000008 |
0.79 |
0.000658 |
0.79 |
0.000497 |
– |
– |
0.87 |
0.000268 |
| ICAM1 |
intercellular adhesion molecule 1 |
3383 |
0.72 |
0.000009 |
0.81 |
0.000002 |
0.52 |
0.000052 |
0.65 |
0.000007 |
– |
– |
– |
– |
– |
– |
– |
– |
| IFI6 |
interferon, α-inducible protein 6 |
2537 |
0.55 |
0.000101 |
0.74 |
0.000007 |
0.61 |
0.000029 |
0.90 |
0.000001 |
– |
– |
– |
– |
– |
– |
– |
– |
| IFIT1 |
interferon-induced protein with tetratricopeptide repeats 1 |
3434 |
– |
– |
– |
– |
– |
– |
1.03 |
0.000027 |
– |
– |
– |
– |
– |
– |
– |
– |
| IFIT2 |
interferon-induced protein with tetratricopeptide repeats 2 |
3433 |
– |
– |
– |
– |
– |
– |
– |
– |
0.47 |
0.000199 |
0.52 |
0.000075 |
– |
– |
– |
– |
| IFNGR2 |
interferon gamma receptor 2 (interferon gamma transducer 1) |
3460 |
– |
– |
0.52 |
0.000070 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| IL18 |
interleukin 18 (interferon-gamma-inducing factor) |
3606 |
1.16 |
0.000013 |
1.02 |
0.000022 |
0.76 |
0.000199 |
0.77 |
0.000131 |
0.93 |
0.000102 |
0.79 |
0.000251 |
– |
– |
0.71 |
0.000595 |
| IL1B |
interleukin 1, β |
3553 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
1.59 |
0.000352 |
2.11 |
0.000034 |
| IL1R2 |
interleukin 1 receptor, type II |
7850 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
1.65 |
0.000433 |
– |
– |
1.91 |
0.000165 |
| IL6 |
interleukin 6 (interferon, β 2) |
3569 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
1.31 |
0.000332 |
| IL6ST |
interleukin 6 signal transducer (gp130, oncostatin M receptor) |
3572 |
– |
– |
0.40 |
0.000286 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| IP6K2 |
inositol hexakisphosphate kinase 2 |
51447 |
– |
– |
0.86 |
0.000041 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| IRF5 |
interferon regulatory factor 5 |
3663 |
– |
– |
– |
– |
0.51 |
0.000033 |
0.61 |
0.000006 |
– |
– |
– |
– |
– |
– |
– |
– |
| ISG20 |
interferon stimulated exonuclease gene 20kDa |
3669 |
– |
– |
– |
– |
– |
– |
– |
– |
0.71 |
0.000539 |
– |
– |
– |
– |
– |
– |
| ITGB1 |
integrin, β 1 (fibronectin receptor, β polypeptide, antigen CD29 includes MDF2, MSK12) |
3688 |
0.28 |
0.000252 |
0.58 |
0.000001 |
0.39 |
0.000015 |
0.33 |
0.000042 |
– |
– |
0.44 |
0.000011 |
0.46 |
0.000012 |
0.40 |
0.000025 |
| JUN |
jun proto-oncogene |
3725 |
– |
– |
0.80 |
0.000048 |
– |
– |
0.86 |
0.000019 |
– |
– |
0.71 |
0.000196 |
– |
– |
– |
– |
| KLRC1 |
killer cell lectin-like receptor subfamily C, member 1 |
3821 |
0.76 |
0.000073 |
0.66 |
0.000150 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| LY96 |
lymphocyte antigen 96 |
23643 |
– |
– |
0.56 |
0.000019 |
0.42 |
0.000160 |
0.68 |
0.000003 |
– |
– |
0.44 |
0.000193 |
– |
– |
0.43 |
0.000280 |
| MAP3K7 |
mitogen-activated protein kinase kinase kinase 7 |
6885 |
– |
– |
– |
– |
0.31 |
0.000213 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| MEF2C |
myocyte enhancer factor 2C |
4208 |
– |
– |
– |
– |
– |
– |
0.32 |
0.000182 |
– |
– |
0.33 |
0.000328 |
– |
– |
– |
– |
| OAS3 |
2'-5′-oligoadenylate synthetase 3, 100kDa |
4940 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
0.44 |
0.000255 |
| OASL |
2'-5′-oligoadenylate synthetase-like |
8638 |
– |
– |
– |
– |
0.28 |
0.000211 |
0.42 |
0.000006 |
– |
– |
– |
– |
– |
– |
– |
– |
| PAG1 |
phosphoprotein associated with glycosphingolipid microdomains 1 |
55824 |
– |
– |
– |
– |
0.58 |
0.000081 |
0.66 |
0.000022 |
– |
– |
– |
– |
0.51 |
0.000486 |
0.59 |
0.000137 |
| PELI3 |
pellino E3 ubiquitin protein ligase family member 3 |
246330 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
0.42 |
0.000345 |
| PIK3C3 |
phosphoinositide-3-kinase, class 3 |
5289 |
0.63 |
0.000103 |
0.68 |
0.000038 |
– |
– |
0.59 |
0.000083 |
– |
– |
– |
– |
– |
– |
– |
– |
| PML |
promyelocytic leukemia |
5371 |
– |
– |
– |
– |
0.70 |
0.000005 |
0.75 |
0.000002 |
– |
– |
– |
– |
– |
– |
– |
– |
| PTPN1 |
protein tyrosine phosphatase, non-receptor type 1 |
5770 |
0.42 |
0.000357 |
0.51 |
0.000064 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| PTPN2 |
protein tyrosine phosphatase, non-receptor type 2 |
5771 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
-0.71 |
0.000545 |
| PVRL2 |
poliovirus receptor-related 2 (herpesvirus entry mediator B) |
5819 |
– |
– |
– |
– |
– |
– |
0.57 |
0.000022 |
– |
– |
– |
– |
– |
– |
0.56 |
0.000065 |
| RAP1A |
RAP1A, member of RAS oncogene family |
5906 |
0.37 |
0.000421 |
0.40 |
0.000187 |
0.41 |
0.000139 |
0.42 |
0.000096 |
– |
– |
– |
– |
– |
– |
– |
– |
| RIPK2 |
receptor-interacting serine-threonine kinase 2 |
8767 |
– |
– |
– |
– |
0.54 |
0.000051 |
0.60 |
0.000016 |
– |
– |
– |
– |
– |
– |
– |
– |
| SHC1 |
SHC (Src homology 2 domain containing) transforming protein 1 |
6464 |
0.58 |
0.000170 |
0.60 |
0.000092 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| SOCS3 |
suppressor of cytokine signaling 3 |
9021 |
– |
– |
0.37 |
0.000153 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| SP100 |
SP100 nuclear antigen |
6672 |
0.46 |
0.000154 |
0.63 |
0.000010 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| STAT1 |
signal transducer and activator of transcription 1, 91kDa |
6772 |
– |
– |
– |
– |
0.32 |
0.000086 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| TICAM1 |
toll-like receptor adaptor molecule 1 |
148022 |
0.46 |
0.000026 |
0.71 |
0.000001 |
0.37 |
0.000080 |
0.58 |
0.000002 |
0.48 |
0.000032 |
0.72 |
0.000001 |
0.57 |
0.000010 |
0.78 |
0.000001 |
| TRAF2 |
TNF receptor-associated factor 2 |
7186 |
-0.39 |
0.000232 |
– |
– |
-0.37 |
0.000242 |
– |
– |
– |
– |
– |
– |
– |
– |
– |
– |
| YWHAB |
tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, β polypeptide |
7529 |
– |
– |
0.41 |
0.000118 |
– |
– |
– |
– |
– |
– |
0.39 |
0.000320 |
– |
– |
– |
– |
| YWHAZ | tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide | 7534 | – | – | – | – | – | – | – | – | 0.51 | 0.000133 | 0.50 | 0.000112 | 0.44 | 0.000389 | – | – |
Table displaying genes from the “Signaling in Immune system” 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 both cell lines the FGS alteration is driven by gene upregulation. P-values per gene can be found in the supplementary data (available in the Supplemental Material and at http://luigimarchionni.org/HDACIs.html).