Expression of Selected Cell Cycle Checkpoint Genes
Supplementary Table 5: Molecules involved in NF-κB activation in C85 cells during maintenance phase of methotrexate-induced senescence.
GeneBank ID / Molecule / Description / Log ratio: / p-value:MTX
48 / R96 / MTX48 / R96
TNF superfamily members
NM_003810 / TNFSF10
(APO2L) / tumor necrosis factor (ligand) superfamily, member 10 / 0,876 / 0,016
NM_005118 / TNFSF15
(TL1) / tumor necrosis factor (ligand) superfamily, member 15 / 1,195 / 0,022
IL-1 molecule
NM_000576 / IL1B / interleukin 1, beta / 0,557 / 0,028
Growth factors
NM_001657 / AREG / amphiregulin (schwannoma-derived growth factor), EGFR ligand / 1,422 / 0,014
NM_006128 / BMP1 / bone morphogenetic protein 1, transcript variant BMP1 / 0,731 / 0,009
NM_001200 / BMP2 / bone morphogenetic protein 2 / 1,048 / 0,017
NM_001432 / EREG / epiregulin, EGFR ligand / 0,723 / 0,001
NM_013962 / NRG1 / neuregulin 1, transcript variant GGF2, ERBB3 ligand / 1,021 / 0,736 / 0 / 0,006
NM_002607 / PDGFA / platelet-derived growth factor alpha polypeptide, transcript variant 1 (RTK) / 2,216 / 2,625 / 0,001 / 0
NM_003236 / TGFA / transforming growth factor, alpha, EGFR ligand / 1,294 / 1,425 / 0,003 / 0,003
TNF receptor / Fas molecules
NM_000043 / FAS / Fas (TNF receptor superfamily, member 6) / 2,017 / 1,798 / 0 / 0,002
NM_002342 / LTBR / lymphotoxin beta receptor (TNFR superfamily, member 3) / 0,566 / 0,006
NM_003844 / TNFRSF10A (DR4) / tumor necrosis factor receptor superfamily, member 10a / 0,743 / 0,003
NM_003842 / TNFRSF10B (DR5) / tumor necrosis factor receptor superfamily, member 10b, transcript variant 1 / 0,755 / 1,079 / 0,001 / 0,002
NM_016639 / TNFRSF12A (TWEAK-R) / tumor necrosis factor receptor superfamily, member 12A / 1,475 / 1,386 / 0,001 / 0
NM_148965 / TNFRSF25 (DR3) / tumor necrosis factor receptor superfamily, member 25 / 0,526 / 0,657 / 0,003 / 0,002
NM_014452 / TNFRSF21 (DR6) / tumor necrosis factor receptor superfamily, member 21 / 0,939 / 2,451 / 0,006 / 0
Toll-like receptors
NM_003263 / TLR1 / toll-like receptor 1 / 1,066 / 0,035
NM_003264 / TLR2 / toll-like receptor 2 / 0,626 / 0,01
NM_003265 / TLR3 / toll-like receptor 3 / 0,932 / 0,005
Interleukin receptors
NM_000418 / IL4R / interleukin 4 receptor, transcript variant 1 / 0,895 / 1,079 / 0 / 0
NM_001560 / IL13RA1 / interleukin 13 receptor, alpha 1 / 0,551 / 0,784 / 0,02 / 0,02
NM_021258 / IL22RA1 / interleukin 22 receptor, alpha 1 / 1,024 / 0,646 / 0 / 0,001
IL1R, TLR and TNFR signaling adaptor molecules
NM_001569 / IRAK1
(not shown in the Figure) / interleukin-1 receptor-associated kinase 1, transcript variant 1 / 0,727 / 0,003
NM_002468 / MYD88
(not shown in the Figure) / myeloid differentiation primary response gene (88) / 1,152 / 1,827 / 0 / 0,001
NM_015093 / TAB2 (MAP3K7IP2) / mitogen-activated protein kinase kinase kinase 7 interacting protein 2 / 0,516 / 0,002
NM_182919 / TICAM1
(TRIF)
(not shown in the Figure) / toll-like receptor adaptor molecule 1, transcript variant 2 / 1,596 / 2,048 / 0 / 0
Integrins
NM_002204 / ITGA3 / integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor), transcript variant a / 1,357 / 1,129 / 0 / 0,009
NM_002211 / ITGB1 / integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12), transcript variant 1A / 0,741 / 1,241 / 0 / 0,011
NM_000211 / ITGB2 / integrin, beta 2 (complement component 3 receptor 3 and 4 subunit) / 0,686 / 0,003
NM_000213 / ITGB4 / integrin, beta 4, transcript variant 1 / 0,87 / 0,776 / 0 / 0,002
NM_002214 / ITGB8 / integrin, beta 8 / 0,647 / 2,376 / 0,001 / 0
Molecules involved in PI3K/AKT-induced NF-κB signaling
NM_005163 / AKT1 / v-akt murine thymoma viral oncogene homolog 1, transcript variant 1 / 0,647 / 0,042
NM_005204 / MAP3K8
(Cot) / mitogen-activated protein kinase kinase kinase 8 / 0,73 / 0,014
NF-κB-inducing kinase (NIK) molecules
NM_003954 / MAP3K14
(NIK) / mitogen-activated protein kinase kinase kinase 14 / 0,562 / 0,919 / 0,006 / 0,011
NM_145686 / MAP4K4
(NIK) / mitogen-activated protein kinase kinase kinase kinase 4, transcript variant 2 / 0,786 / 0,451 / 0 / 0,011
Molecule of NF-κB activator
NM_003639 / IKBKG
(IKKγ) / inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma / 0,915 / 0,003
NF-κB transcriptional complex molecules
NM_002502 / NFKB2 / nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100) / 0,568 / 0,001
NM_006509 / RELB / v-rel reticuloendotheliosis viral
oncogene homolog B, nuclear factor of kappa light polypeptide gene enhancer in B-cells 3 (avian) / 0,902 / 1,465 / 0 / 0
NF-κB effector molecules
NM_138578 / BCL2L1
(Bcl-xL) / BCL2-like 1 nuclear gene encoding mitochondrial protein, transcript variant 1 / 1,025 / 0,948 / 0,005 / 0,001
NM_001165 / BIRC3
(cIAP) / baculoviral IAP repeat-containing 3, transcript variant 1 / 1,816 / 4,119 / 0,003 / 0
NM_002985 / CCL5
(RANTES) / chemokine (C-C motif) ligand 5 / 1,056 / 1,431 / 0,002 / 0,036
NM_053056 / CCND1 / cyclin D1 / 1,078 / 0,002
NM_001511 / CXCL1 / chemokine (C-X-C motif) ligand 1 (melanoma growth stimulating activity, alpha) / 2,792 / 0,001
NM_002090 / CXCL3 / chemokine (C-X-C motif) ligand 3 / 1,937 / 0,004
NM_000201 / ICAM1 / intercellular adhesion molecule 1 (CD54), human rhinovirus receptor / 0,69 / 1,044 / 0,002 / 0,002
NM_000625 / NOS2A / nitric oxide synthase 2A (inducible, hepatocytes), transcript variant 1 / 0,985 / 3,295 / 0,002 / 0
NM_000930 / PLAT / plasminogen activator, tissue, transcript variant 1 / 1,188 / 0,018