Datasets:

Venkatachalam
/

aging_reg_dataset

gene_name string	gene_id string	category string	cell_name string	tissue_type string	phenotype string	aging_type string	experiment string	description string	target_gene string	regulatory_type_of_target_gene string	target_gene_experiment string	target_gene_description string	regulatory_pathway string	regulatory_type_of_pathway string	pathway_experiment string	pathway_description string	species string	experimental_category string	aging_characteristic string	pmid int64	source string	BrdU_assay int64	CCK_8_assay int64	Cell_counting int64	Cell_morphological_analysis int64	Cell_proliferation_assay int64	Cell_viability_assay int64	Colony_formation_assay int64	Colony_formation?assay int64	EdU_assay int64	Flow_cytometry int64	Immunofluorescence int64	Knockdown int64	MTT_assay int64	RT_PCR int64	SA__Gal_activity_assay int64	SA__gal_activity_assay int64	SAHF int64	Telomere_length_assay int64	Western_blot int64	qPCR int64	qRT_PCR int64
MYC	4609	protein coding	TRE293	--	Aging	Prevent	SA--gal activity assay//Western blot	TRE293 cells treated with c-Myc shRNA demonstrated significant changes in senescence and induced the p53/p21CIP1 pathway.	BAG2	Downregulation	Western blot//BrdU assay//SA-¦Â-gal activity assay	In cells that demonstrated high levels of BAG2 in response to SP1 over-expression, transfection of c-Myc was shown to abrogate the BAG2 mRNA levels in a concentrationdependent manner.	p53-p21	Upregulation	Western blot	TRE293 cells treated with c-Myc shRNA demonstrated significant changes in senescence and induced the p53/p21CIP1 pathway.	Human	HL	cellular senescence	22,146,591	Gene	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0
NLRX1	79671	protein coding	HCCLM3	--	Hepatocellular carcinoma	Accelerate	CCK-8 assay//SA--gal activity assay	We found that NLRX1 overexpression could hinder cell proliferation in HCCLM3 cells, while knocking down NLRX1 in Huh7 resulted in significant higher proliferation rates. NLRX1-OE significantly increased SA-¦Â-gal activity, indicating a higher proportion of aging in NLRX1-OE cells compared to cells transfected with vect...	p21	Upregulation	Western blot//RT-PCR	We found that NLRX1-OE could effectively upregulate P21 expression, and expressions of downstream targets of P21 including CDK1 and CDK2 were significantly repressed due to high level of P21 expression caused by NLRX1 overexpression, while knocking down NLRX1 in Huh7 resulted in increased expression of CDK1 and CDK2.	PI3K-Akt	Downregulation	Western blot	NLRX1-OE markedly inhibited the phosphorylation of mTOR, indicating that NLRX1 suppresses PI3K-AKT signaling.	Human	HL	cellular senescence	29,482,578	Gene	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
PRKAA1	5562	protein coding	NIH-3T3	--	Aging	Prevent	SA--gal activity assay	Next, we observed that when the H2O2-treated cells were incubated with medium containing Met and BBR, there was a dose-dependent decrease in the percentage of SA-¦Â-Gal-positive cells, which was similar to that caused by rapamycin treatment.As expected, when combined with CC, the effects of Met or BBR on senescence pre...	LC3//p62	Downregulation//Downregulation	Western blot	With Western blot assay, we found that both Met and BBR alleviated the H2O2-induced accumulation of the LC3 and p62 proteins, and this alleviation was consistent with the effect of rapamycin.	mTOR	Downregulation	Western blot	Moreover, we found that BBR treatment significantly suppressed mTOR phosphorylation in senescent cells, similar and even stronger than that induced by rapamycin and insulin as an mTOR activation control.	Human	L	delay aging	26,890,602	Gene	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
IGFBP7	3490	protein coding	MDA-MB-231	--	Breast cancer	Accelerate	Cell morphological analysis//Flow cytometry//SA--gal activity assay	IGFBP7 treatment of MDA-MB-231 cells increased the percentage of cells in G1 (73.86%) compared to untreated cells (54.14%), with a consequent decrease in the percentage of cells in S phase (15.85% in IGFBP7-treated cells versus 33.8% in untreated controls).We found that MDA-MB-231 cells treated with IGFBP7 for 2 days u...	p21//p53	Upregulation//Upregulation	Western blot	In agreement with this, we found that IGFBP7-treated MDAMB-231 cells had higher p21 and p53 expression than untreated cells.	p38 MAPK	Upregulation	Western blot	Levels of phosphorylated p38 MAPK were dramatically increased by IGFBP7 treatment.	Human	L	apoptosis	21,997,538	Gene	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0
MEF2A	4205	protein coding	HUVEC	Human umbilical vein	Cardiovascular disease	Prevent	Cell viability assay//SA--gal activity assay	The percentage of senescent phenotype cells in MEF2A overexpression group was significantly lower than that in the empty plasmid group and the MEF2A mutant group (pc-gab-MEF2A-MV30).MEF2A overexpression in HUVECs significantly increased cell viability.	p53	Downregulation	Western blot	The level of p53 was significantly decreased?in the MEF2A-overexpression HUVECs.	PI3K-p-AKT-SIRT1	Upregulation	qRT-PCR//Western blot	PIK3CA, PIK3CG, and SIRT1 mRNA levels were significantly up-regulated in the MEF2Aoverexpression HUVECs, and the protein levels of PIK3CA, PIK3CG, SIRT1, and p-Akt notably increased .	Human	L	Others	31,182,679	Gene	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
MIR584	693169	ncRNA	MGC803,SGC-7901	--	Gastric cancer	Accelerate	SA--gal activity assay//Western blot	The miR-584- 5p-mimic-transfected cells showed strong blue SA-¦Â-gal staining, while only scattered SA-¦Â-gal-positive cells were detected in miR-584-5p-inhibitor-transfected group compared with the corresponding control cells.The expression of p53, p21 and p16 was enhanced after miR584-5p-mimic-transfection. Conversel...	WWP1//p53	Downregulation//Upregulation	SA-¦Â-gal activity assay//Western blot//Flow cytometry	Intriguingly, co-transfection of MGC803 cells with miR-584-mimic and either LV-WWP1 or LV-NC showed that ectopic expression of WWP1 effectively reversed the promotion of cellular senescence resulting from miR-584-5p overexpression. Similarly, the effects of miR584-5p knockdown in SGC7901 were counteracted by WWP1 downr...	TGF¦Â	Activation	Western blot//Immunofluorescence	Western blot analysis of the expression of WWP1 and key proteins involved in TGF¦Â signaling pathway showed that the protein levels of T¦ÂR1, Smad2, Smad4, and the CDK inhibitor p15 were increased after miR-584-5p-mimic transfection, while the opposite effects were observed after miR-584-5p-inhibitor transfection.Howe...	Human	HL	cellular senescence	28,431,583	Gene	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0
TP53	7157	protein coding	EJ	--	Aging	Accelerate	Knockdown//SA--gal activity assay	The adenovirus-mediated expression of p53 in EJ p53-null human bladder cancer cells promoted remarkable morphological changes and senescence-associated ¦Â-galactosidase (SA-¦Â-gal) activity, which are features of premature senescence phenotypes,within 6 days. Irreversible growth arrest, which is characteristic of cellu...	p21//Akt	--//Activation	SA-¦Â-gal activity assay//Western blot	P53-mediated Akt activation and the inhibition of p53-induced SA-¦Â-gal activity by LY294002 treatment were also observed in H1299 human lung cancer cells .Akt and p21 separately regulate p53-induced ROS increases and cell cycle arrest, respectively.suppression of the induction of p21 expression successfully inhibited ...	NF-¦ÊB-NOX4	--	SA-¦Â-gal activity assay//ChIP//RT-PCR	NOX4 knockdown resulted in the significant suppression of p53-induced SA-¦Â-gal activity but did not affect the loss of proliferation.Importantly, the chromatin immunoprecipitation (ChIP) assay results indicated that NF-kB binding to the putative binding site on the NOX4 promoter was enhanced by p53 expression, but thi...	Human	L	cellular senescence	28,691,365	Gene	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0
NAMPT	10135	protein coding	MEF	--	Aging	Prevent	SA--gal activity assay	Over- expression of NAMPT in MEF cells slows down cellular senescence.Percentage of cells that is positive for SA- ¦Â- Gal activity in all Wt- MEF cells was dramatically increased from passage 6, consistent with the timing of CCP in Wt- MEF cells.we measured the expression level of several senescence marker genes. p16I...	SIRT1	Upregulation	qRT-PCR	We finally examined whether SIRT1 activity is enhanced in response to NAMPT over- expression. Although SIRT1 has been shown to regulate cellular proliferation and senescence, this function is dependent on the robustness of the intrinsic NAMPT activity and NAD+ content. SIRT1 is also vital in regulating FOXO- mediated a...	--	--	--	--	Human	L	cellular senescence	29,178,516	Gene	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
SIRT1	23411	protein coding	WI-38	--	Aging	Prevent	BrdU assay//SA--gal activity assay	As observed for the growth curves,expression of SIRT1 alone does not significantly affect the percentage of cells in S phase or the percentage of SA-¦Â-gal-positive cells when compared with control infected cells. However, expression of PML IV results in a striking decrease of BrdU-positive cells and a huge increase in...	p53	Binding	Pull-down assay	We performed pull-down assays with either full-length GST¨Cp53 or a series of GST¨Cp53 fusions expressing only the N-terminal, middle or C-terminal regions of the protein, and in vitro translated SIRT1. We observed specific binding of SIRT1 to full-length p53 as well as to GST¨Cp53(290¨C393), while weaker binding was s...	--	--	--	--	Human	HL	cellular senescence	12,006,491	Gene	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
CDK5	1020	protein coding	Saos-2	--	Aging	Accelerate	Knockdown//SA--gal activity assay	SiCDK5 or dnCDK5 partially inhibited this activity, and interestingly, CDK5 overexpression enhanced the number of SA-¦Â-Gal-positive cells.	Rac1	Downregulation	SA-¦Â-gal activity assay	In the presence of activated Rac1, most pRb induction of SA-¦Â-Gal was compromised, a phenotype that was exacerbated by expression of dnCDK5, roscovitine, or siCDK5 treatment . Coexpression of CDK5 with pRb and RacV12 resulted in a partial rescue of SA-¦Â-Gal expression, suggesting that CDK5 might be antagonizing some ...	--	--	--	--	Human	L	cellular senescence	15,024,070	Gene	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0
MORC3	23515	protein coding	WI-38	--	Aging	Accelerate	SA--gal activity assay//Western blot	The percentage of SA-¦Â-Gal¨Cpositive cells infected with the MORC3-retrovirus vector (51.0¡À5.1%) was significantly greater than that of controls infected with vector alone (2.3¡À0.8%). MORC3 expression also strongly induced p16, another senescence marker.	p53	Activation	Luciferase reporter assay	FLAG-MORC3 expression enhanced transcriptional activation by endogenous p53 of a reporter containing 12 p53-responsive elements (PG12S) in a dose-dependent manner, but not activation of a reporter containing 14 mutated responsive elements (MG14S).	--	--	--	--	Human	L	cellular senescence	17,332,504	Gene	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0
IGFBPL1	347252	protein coding	MCF-7	--	Aging	Accelerate	Cell counting//Flow cytometry//SA--gal activity assay	Cell proliferation of MCF-7 cells was severely inhibited following IGFBP-rP1 transfection,whereas there were indistinguishable differences in cell proliferation between the control vector-transfected and the untransfected cells. On day 7, the IGFBP-rP1-transfected MCF-7 cells had an enlarged flat morphology,characteris...	p21	Upregulation	Knockdown//Western blot//Cell counting//SA-¦Â-gal activity assay	Basal and IGFBP-rP1-inducible p21 levels deceased dramatically in p21 knockdown MCF-7 cells.Accordingly, IGFBP-rP1-mediated pRb dephosphorylation was substantially reduced in these cells. We also examined cell proliferation and cellular senescence in response to IGFBP-rP1 in parental and p21 knockdown MCF-7 cells. The ...	--	--	--	--	Human	L	cellular senescence	22,392,074	Gene	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0
GADD45G	10912	protein coding	SK-Hep-1,SMMC-7721	--	Hepatocellular carcinoma	Accelerate	Cell morphological analysis//SA--gal activity assay	In agreement with previous observation, we confirmed that the induction of GADD45G expression in Sk-Hep1 cells (Tet-on-GADD45G-Sk-Hep1) and SMMC-7721 cells (Tet-on-GADD45G-SMMC-7721) resulted in characteristic morphological changes common in senescent cells and a dramatic increase in the proportion of SA-¦Â-Gal-stainin...	SIP1	Upregulation	qRT-PCR//Western blot	Surprisingly, we found that the levels of SIP1 mRNA were significantly elevated in the cells upon GADD45G induction.The change in SIP1 mRNA expression was also reflected at the protein levels in Sk-Hep1 and SMMC-7721 cells upon GADD45G induction. In addition, GADD45G-induction of SIP1 expression similarly occurred in H...	--	--	--	--	Human	HL	cellular senescence	26,378,039	Gene	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
HMGA2	8091	protein coding	WI-38	--	Retinoblastoma	Accelerate	SA--gal activity assay//Western blot//qPCR	We found that the ectopic overexpression of HMGA2 led to elevated SA-¦Â-galactosidase staining and acquisition of the SAHF-like chromatin foci in the nuclei. Meanwhile, the expression levels of the senescence-related proteins, such as p16, p21, p53 and phosphorylated p53, were prominently increased. The transcription l...	E2F	Downregulation	Western blot	Surprisingly, both HMGA2 and Rb were detected in the same protein complex in our model (data not shown), together with the down-regulation of E2F target genes in WI38 cells in response to HMGA2 overexpression.	Rb	--	Western blot//qPCR//RT-PCR//Immunofluorescence	To further test whether Rb is a crucial factor in SAHF formation induced by HMGA2, E7 protein was used as the specific inhibitor of Rb , and the effect of E7 protein on the degradation of Rb was confirmed by Western blotting . Interestingly, we found that E7 protein was able to partly abolish the SAHF formation induced...	Human	L	cellular senescence	23,969,248	Gene	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1	0
RRAD	6236	protein coding	NHF	--	Aging	Prevent	Knockdown//SA--Gal activity assay	We found that RRAD knockdown increased the ratio of senescent cells in both H2O2- and IR-induced senescence as determined by SA-¦Â-gal staining assay and BrdU incorporation assay.	p53//NF-¦ÊB	--//--	Knockdown//CHIP-Seq//qRT-PCR	We established p53 knockdown NHFs by a lentiviral based approach for the following functional assay. In OIS, p53 knockdown diminished H-Ras-induced RRAD up-regulation.p53 knockdown also abolished H 2O2-induced RRAD expression.In a published ChIP-Seq data set of IMR-90 cells, we noted that both p53 and NF-¦ÊB bind to th...	--	--	--	--	Human	HL	cellular senescence	30,391,675	Gene	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0
ING1	3621	protein coding	2BS	--	Aging	Accelerate	Immunofluorescence//SA--gal activity assay//SAHF	The results showed that 2BS cells overexpressing of p33ING1befficiently induced the expression of SA-¦Â-gal activity, flattened senescent cell morphology, and SAHF DNA staining pattern which is indicated by co-localization with H3K9Me3.	p16	Upregulation	qPCR//Western blot//Luciferase reporter assay	qPCR and Western blot results showed that introduction of p33ING1b upregulated p16INK4amRNA and protein levels.Moreover, p16INK4apromoter activity was upregulated by p33ING1b.The results showed that cells treated with p33ING1balone revealed strong SA-¦Â-gal staining and p16 increasing, whereas cells doubly treated with...	--	--	--	--	Human	L	cellular senescence	21,896,275	Gene	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	1	0	0	0	0
TWIST	100303576	protein coding	SW48	--	Aging	Prevent	BrdU assay//SA--gal activity assay	Higher percentage of SA-¦Â-gal-positive cells was found in the Sh-TWIST transfectants (filled columns) compared with the controls (open columns) in response to both agents in a dose-dependent manner. This was associated with a decreased cell proliferation rate examined by BrdUrd incorporating assay.These results sugges...	p14//cH2AX	Downregulation//Upregulation	Western blot	We also found that the p14ARF expression levels were much lower in the TWIST over-expressing cells, either before or after exposure to H2O2 and CP (right panels), compared with the vector control, confirming the negative effect of TWIST on p14ARF. In addition, the p53 and p21 levels were lower in the TWIST over-expres...	Mdm2-p53	--	Western blot	Western blotting analysis showed that the expression levels of p14ARF were much higher in the Sh-TWIST transfectants after exposure to H2O2 or CP in a dose-dependent manner. In contrast, the level of MDM2 was decreased, which was associated with up-regulation of p53 and p21, suggesting that inactivation of TWIST promot...	Human	L	cellular senescence	17,690,110	Gene	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
CAV1	857	protein coding	MEF	--	Aging	Accelerate	SA--gal activity assay//Western blot	In contrast, wild type MEFs over-expressing caveolin-1 developed a senescent phenotype 4 days after oxidative stress, as determined by senescent-associated ¦Â-galactosidase staining and p21 upregulation.	SIRT1	Binding	Pull-down assay	To determine whether Sirt1 binds directly to caveolin-1, we performed GST pulldown assays using recombinant Sirt1. We found that human recombinant Sirt1 bound to caveolin 1 (residues 82¨C101)-GST.The incubation with the purified GST-Cav-1 (82¨C101) peptide inhibited Sirt1 activity by- 45% compared to GST alone.	p53	--	Pull-down assay//IP//Western blot	We found that human recombinant Sirt1 bound to caveolin 1. However, Sirt1 strongly interacted with caveolin-1 72 hours after stimulation of WI-38 cells with sublethal doses of hydrogen peroxide that we have previously shown induce premature senescence.In contrast, free radicalinduced acetylation of p53 was significantl...	Human	L	cellular senescence	25,512,378	Gene	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0
NQO1	1728	protein coding	2BS	--	Aging	Accelerate	BrdU assay//Cell proliferation assay//SA--gal activity assay//qRT-PCR	NQO1 depletion resulted in continuous cell growth compared with corresponding control lentiviral vector (Cont) infected cells . In addition, the morphology changed during the OIS, with senescent cells exhibiting the typical enlarged and flattened shape. Five days after introducing RasG12V, NQO1 depleted 2BS cells showe...	p53	Binding	Western blot	To test the relevance of NQO1-p53 binding in OIS, p53 was immunoprecipitated in 2BS cells. Western blot analysis verified that NQO1 specifically interacted with p53 in premature senescence.	Nrf2-Keap1	--	Western blot//CHIP//qPCR//Knockdown//Luciferase reporter assay	MAF and KEAP1 were immunoprecipitated from 2BS cells, and western blot analysis verified that during OIS NRF2 was dislocated from KEAP1 and bound with MAF, suggesting that OIS activates NRF2 and results in NRF2-mediated up-regulation of NQO1. Next, we detected whether NRF2 bound to the endogenous NQO1 promoter by chrom...	Human	HL	cellular senescence	26,078,718	Gene	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1
RSL1D1	26156	protein coding	2BS	--	Aging	Prevent	SA--gal activity assay	No SA-¦Â-gal activity was observed in CSIG transfected 2BS and early-passage cells, whereas CSIG-CT transfected 2BS cells were strongly stained, as were late-passage (senescent) 2BS control cells.	PTEN	Downregulation	Western blot	As expected, CSIG overexpression diminished PTEN abundance.	--	--	--	--	Human	L	cellular senescence	26,686,419	Gene	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
S100A13	6284	protein coding	IMR-90	--	Aging	Accelerate	Knockdown//SA--gal activity assay	S100A13 overexpression promotes, whereas S100A13 knockdown delays replicative cellular senescence in IMR9 cells. S100A13 mutant significantly decreased the percentage of SA-¦Â-gal positive staining cells.	IL-1	Upregulation	Flow cytometry//Immunoblotting	FACS analysis of cell surface-bound IL-1¦Á showed that S100A13 overexpression significantly enhanced IL-1¦Á levels compared to empty vector control cells.	--	--	--	--	Human	L	cellular senescence	30,670,674	Gene	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0
TRIB2	28951	protein coding	LoVo	--	Colorectal cancer	Prevent	Cell morphological analysis//Flow cytometry//Knockdown//SA--gal activity assay	TRIB2 knockdown cells showed higher rates of flat and enlarged senescence-like morphology.Cell cycle distribution of the cells transfected with TRIB2-specific siRNA were determined by flow cytometry.TRIB2 knockdown dramatically increased the G0/G1-phase ratios and reduced the S-phase ratios. The level of SA-¦Â-gal (a b...	--	--	--	--	AP4-p21	--	Western blot//RT-PCR//Luciferase reporter assay//IP//CHIP	Silencing TRIB2 dramatically up-regulated p21 expression, inhibited cell growth, induced cell cycle arrest and enhanced cellular senescence. The luciferase assay indicated TRIB2 inhibited p21 promoter activities in an AP4-dependent manner. We then performed CCK8 and SA-¦Â-gal staining analysis to examine the effects of...	Human	L	cellular senescence	30,541,550	Gene	0	0	0	1	0	0	0	0	0	1	0	1	0	0	0	1	0	0	0	0	0
LBR	3930	protein coding	TIG-7	--	Aging	Prevent	Knockdown//SA--Gal activity assay	We also found that the cells transfected with the LBR knockdown vector were stained with SA-¦Â-gal, which observation suggested that knockdown of LBR induced cellular senescence in TIG-7 cells.	--	--	--	--	--	--	--	--	Human	L	cellular senescence	30,615,890	Gene	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0
PTEN	5728	protein coding	MCF-7	--	Aging	Prevent	Knockdown//SA--Gal activity assay	The SA-¦Â-Gal positivity of PTEN KO MEFs was dramatically attenuated in Torin1-treated cells compared to Rapa-treated cells.	--	--	--	--	p53-p21	--	Western blot	PTEN-depleted MCF7 cells displayed prematurely senescent phenotypes in a p53/p21-dependent manner.	Human	L	cellular senescence	30,337,688	Gene	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0
MDM2	4193	protein coding	HCT116	--	Werner syndrome	Accelerate	SA--Gal activity assay	Ectopic expression of WRN attenuates the senescent phenotype induced by Etoposide,as shown by senescence-associated ¦Â-galactosidase (SA-¦Â-Gal) activity.	WRN	--	IP	WRN and MDM2 association was detected in co-transfected 293T cells by reciprocal immunoprecipitations.	--	--	--	--	Human	L	cellular senescence	30,532,073	Gene	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
ASPH	444	protein coding	FOCUS,HuH-7,HepG2	--	Hepatocellular carcinoma	Prevent	Knockdown//SA--Gal activity assay	Knockdown or knockout of ASPH, caused substantial increase in ¦Â-gal staining as a marker for the cells undergoing senescence.	GSK3¦Â	--	Western blot//IP//Immunoblotting	We found a significant increase of phospho-GSK3¦Â(inactivated form) with equal protein expression of GSK3¦Â when comparing the shASPH to the shLuc control.Direct protein-protein interaction between GSK3¦Âand ASPH was demonstrated by co-immunoprecipitation (IP).Immunoblotting with anti-GSK3¦Â revealed that GSK3¦Â bou...	--	--	--	--	Human	L	cellular senescence	26,683,595	Gene	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0
RXRA	6256	protein coding	MRC-5	--	Aging	Prevent	Knockdown//SA--Gal activity assay	RXRA knockdown decreased cell proliferation as we observed a drop in the expression of the cell proliferation marker Ki©\67 and a decrease in the number of cells .Importantly, RXRA knockdown also caused an increased SA©\¦Â©\galactosidase activity.	p53	--	Knockdown//Western blot	Using the same approach,we further showed that cellular senescence induced by RXRA knockdown was also dependent on MCU and p53.	ITPR2-MCU	--	Knockdown//qRT-PCR//Western Blot//SA-¦Â-Gal activity assay	To assess whether this senescent phenotype was dependent on ITPR2, we knocked down ITPR2 together with RXRA.ITPR2 knockdown impaired the upregulation of CDKN1A and GDF15 . The proliferation arrest and the increase in SA©\¦Â©\galactosi-dase activity triggered by RXRA knockdown were alsoimpaired. Similar observations wer...	Human	HL	cellular senescence	30,216,632	Gene	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0
LRRK2	120892	protein coding	SH-SY5Y	--	Parkinson¡¯s disease	Accelerate	Western blot	Up-regulated ¦Â-galactosidase protein levels in G2019S-mediated phosphomimetic p53 and overexpression of p21 or G2019S LRRK2.	--	--	--	--	p53-p21	Upregulation	Western Blot//SA-¦Â-Gal activity assay	We observed a significant increase in ¦Â- gal protein level with the expression of T304/377D p53 (TD-p53) compared to that in the vector and WT-p53 in dSH-SY5Y cells . In addition, the overexpression of p21 and G2019S LRRK2 in dSH-SY5Y cells resulted in significant increases in ¦Â-gal protein expression. We found that ...	Human	L	cellular senescence	30,712,480	Gene	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0
TSHB	7252	protein coding	--	Adipose	Aging	Prevent	RT-PCR//Telomere length assay	In euthyroid morbidly obese subjects,both SAT and VAT TSHB gene expression was negatively associated with markers of AT senescence (TNF , TP53, BAX and DBC1). Confirming these findings, SAT TSHB mRNA was positively linked to telomere length in a subgroup of consecutive subjects , suggesting decreased senescence with le...	--	--	--	--	--	--	--	--	Human	L	cellular senescence	30,448,824	Gene	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0
FXR1	8087	protein coding	UMSCC74A,UMSCC74B	--	Oral cancer	Prevent	Flow cytometry//Knockdown//SA--Gal activity assay	To investigate the underlying mechanism of reduction in number of viable cells following FXR1 KD, we performed cell cycle analysis of the FXR1 KD and control cells by flow cytometry. FXR1 KD induces cell cycle arrest in G /G1 providing evidence that FXR1 might regulate cell division in oral cancer.Silencing of FXR1 in ...	TERC	--	Luciferase reporter assay	When full-length and truncated TERC (28 base deletion at 5¡¯-end,TERCmut£© are used for luciferase assay,TERC exhibits increased luciferase activity in control cells compared to TERCmut. However, in FXR1 KD cells, TERC exhibits a decreased luciferase activity compared to TERCmut indicating that FXR1 binds to specific G...	p53-p21	--	RT-PCR//Western Blot	Upregulation ofp53 and p21 protein levels are observed in the absence of FXR1 in WT p53 cell line.RT-PCR¡¢Western Blot£ºoverexpressed FXR1 in HNSCC destabilizes p21 mRNA and reduces its protein expression.concurrent overexpression of p21 and silencing of TERC significantly promoted senescence evidenced by staining of S...	Human	HL	cellular senescence	27,606,879	Gene	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0
CDKN2A	1029	protein coding	DFC	--	Aging	Accelerate	SA--Gal activity assay//Western blot	P16 gene silencing reduces the number of senescent cells.Only the protein expression of P16 in DFCs increased successively and significantly while the expression of all other examined cell cycle proteins including that of P21 was down-regulated significantly at higher cell passages.	--	--	--	--	--	--	--	--	Human	HL	cellular senescence	28,770,470	Gene	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0
SIRT6	51548	protein coding	2BS	--	Aging	Prevent	Colony formation?assay//Flow cytometry//RT-PCR//Western blot	Western blot analysis revealed that the expression of SIRT6 was high in young cells, but decreased significantly during cellular senescence. Consistently, RT-PCR analysis revealed that mRNA levels of SIRT6 decreased in senescent cells .Another hallmarker of senescent cells is the ability of colony formation. We observe...	p27	--	Western blot//RT-PCR//SA-¦Â-gal activity assay//Co-IP//Pull-down assay	In addition,SIRT6 silencing did not alter the protein levels of p16, p21, p53 and PTEN, but markedly increased p27 protein levels. Moreover, the real-time PCR analysis demonstrated similar p27 mRNA levels in both SIRT6-overexpressing and knockdown cells, suggesting that SIRT6 might decrease the p27 protein levels but n...	--	--	--	--	Human	HL	cellular senescence	27,794,562	Gene	0	0	0	0	0	0	0	1	0	1	0	0	0	1	0	0	0	0	1	0	0
TIMELESS	8914	protein coding	2BS	--	Aging	Prevent	Western blot//qRT-PCR	The expression of circadian protein TIMELESS was down-regulated during the onset of OIS, while other members of circa-dian clock showed no significant changes in their expression.The downregulation of TIMELESS was also confirmed inreplicative senescence and H2O2 induced senescence,suggesting TIMELESS downregulation mig...	E2F1	--	Knockdown//Luciferase reporter assay//CHIP//qRT-PCR//Western blot	Chromatin immunoprecipitation (ChIP) assay was utilized to confirm the binding of E2F1 to the endogenous TIMELESS promoter.Interaction between E2F1 and TIMELESS promoter region was detected by qRT-PCR.As expected, interaction between E2F1 and TIMELESS promoter was observed in young 2BS cells.Furthermore, the mutation i...	--	--	--	--	Human	L	cellular senescence	30,100,061	Gene	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1
TSLP	85480	protein coding	BEAS-2B	--	Asthma	Accelerate	SA--gal activity assay//Western blot	Specifically,senescent cells increased >15 fold upon treatment with 1.5ng/ml TSLP.There was increased expression of SA-¦Â-gal and decreased Ki67 expression in BEAS-2B cells upon TSLP treatment.	--	--	--	--	--	--	--	--	Human	L	cellular senescence	24,167,583	Gene	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0
UHRF1	29128	protein coding	2BS,IMR-90	--	Aging	Prevent	CCK-8 assay//EdU assay//Knockdown//SA--gal activity assay	Cell proliferation rates decreased in UHRF1 shRNA-infected cells. Growth curves of UHRF1 shRNA-infected 2BS cells or IMR9 cells were determined by CCK8 assay.The percentage of cells incorporating EdU also decreased in UHRF1 shRNA-infected 2BS cells or IMR9 cells. SA-¦Â-gal activity staining increased in UHRF1 shRNA-inf...	PIM1	--	IP	In reciprocal immunoprecipitations, PIM1 was observed presentingin UHRF1 immunoprecipitates.	--	--	--	--	Human	HL	cellular senescence	28,394,343	Gene	0	1	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0
WNT7A	7476	protein coding	A549	Lung	Lung cancer	Accelerate	CCK-8 assay//SA--gal activity assay	Histological analysis of the lung sections of the wild-type and Wnt7a-null mice showed no difference in basal staining for SA-¦Â-gal activity. However, a large number of SA-¦Â-gal-positive cells, predominantly in the tumor area, were observed in lung sections of the wild-type mice after urethane treatment, whereas Wnt7...	--	--	--	--	SKP2-p27-pRb	--	Western Blot	Consistent with the changesin SKP2 and p27kip1 expression, the levels of phosphorylated(p-Rb-S780) retinoblastoma proteins in Wnt7a-null mice were dramatically increased as well . Cyclin D1, which is critical for Ser780 phosphorylation of Rb ,was also upregulated in Wnt7a-null mice, along with CDK2 andCDK6, components ...	Human	HL	cellular senescence	25,728,679	Gene	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
SPHK1	8877	protein coding	Adipose stromal cell	--	Aging	Prevent	BrdU assay//SA--gal activity assay	A SPHK1 inhibitor, significantly reduced the incorporation of BrdU into cellular DNA compared to control cells,indicative of the lowered proliferative ability.As with high-passage cells,SPHK1-depleted or SKI-treated hAD-SCs underwent accelerated cellular senescence as evidenced by higher SA-¦Â-gal activity.	S1P	--	SA-¦Â-gal activity assay//BrdU assay	To test this hypothesis, we investigated whether SPHK1 knockdown-induced cellular senescence could be attenuated by inhibition of ceramide synthesis or exogenous supple- mentation with S1P during cell culture. BrdU incorporation assays showed that the proliferation impeded by shRNA- mediated silencing of SPHK1 could no...	--	--	--	--	Human	L	cellular senescence	30,885,289	Gene	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
IGF1	3479	protein coding	VSMC	--	Aging	Accelerate	SA--gal activity assay	We observed a strong induction of SA-¦Â-gal activity following IGF-I stimulation in the confluent cells	--	--	--	--	ROS-p53	--	Immunoblotting//SA-¦Â-gal activity assay	We examined the involvement of ROS in the induction of cellular senescence by IGF-I.Treatment with an ROS scavenger, N-ace-tylcysteine (NAC), significantly suppressed the IGF-I-induced increase in SA-¦Â-gal activity. Furthermore, NAC treatment also suppressed the induction of cH2AX, p53, and p21 proteins, indicating th...	Human	L	cellular senescence	22,877,754	Gene	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
SETD8	387893	protein coding	PC-3	--	Aging	Prevent	Flow cytometry//Knockdown//SA--gal activity assay	In PC3 cells harboring SETD8-specific siRNAs,we detected a greater extent of ¦Â-gal-positive staining,cell proliferation arrest,nuclear area enlargement,G2/M arrest .Consistent with its known pro-proliferation role,overexpression of SETD8 in the absence of dox treatment elevated the rate of cell growth.In dox-treated c...	PPARc//p21	--//Downregulation	qRT-PCR//SA-¦Â-gal activity assay//CHIP//Flow cytometry	In support of its role as an upstream regulator, ectopic overexpression of PPARc led to an increase in the expression of SETD8 and H4K20me1, and conversely a decline in the p21 mRNA levels.To further demonstrate the role of PPARc in controlling senescence, we showed that overexpression of PPARc alleviated the extent of...	--	--	--	--	Human	HL	cellular senescence	28,514,051	Gene	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	1	0	0	0	0	0
YPEL3	83719	protein coding	MCF-7,U2OS	--	Aging	Accelerate	Colony formation assay//SA--gal activity assay	Using a colony formation assay,both cell lines showed considerably fewer colonies when expressing YPEL3 compared with cells not induced to express YPEL3. Growth suppression was also observed after shorter time periods of YPEL3 induction. Due to difficulties in the long-term growth of YPEL3 expressing cells, the inabili...	p53	--	Dual-Luciferase reporter assay//Immunoblotting	The level of YPEL3 mRNA induction was significantly reduced in doxorubicintreated Hct116 cells lacking p53 .Cotransfection of the YPEL3-luciferase reporter with wild-type p53 in either Hct116?/?p53 or H1299 cells led to an increase in YPEL3 promoter activity .Having established that the YPEL3 promoter could be activate...	--	--	--	--	Human	HL	cellular senescence	20,388,804	Gene	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0
IFNG	3458	protein coding	HUVEC	--	Aging	Accelerate	Flow cytometry//MTT assay//SA--gal activity assay	Cell proliferation decreased slightly with IFN-¦Ã treatment in time- and dose-dependent manners. A decrease in cell proliferation by IFN-¦Ã treatment for 3 days was statistically significant (p < 0.05). The induction of cellular senescence by prolonged treatment with IFN-¦Ã was confirmed by an increase in SA-¦Â-gal-pos...	p53	--	Knockdown//SA-¦Â-gal activity assay//Western blot	Prolonged stimulation of IFN-¦Ã in the p16-knockdown (p16sh) cells increased SA-¦Â-gal activity staining to a level similar to that in control cells. In contrast, no increase in SA-¦Â-gal staining was observed in the p53-knockdown (p53sh) cells following prolonged stimulation with IFN-¦Ã. We reproducibly noticed an inc...	--	--	--	--	Human	L	cellular senescence	19,071,156	Gene	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	1	0	0	0	0	0
HDAC4	9759	protein coding	2BS	--	Aging	Prevent	Flow cytometry//Knockdown//MTT assay//SA--gal activity assay//Western blot//qRT-PCR	The overexpression and knockdown of HDAC4 were confirmed by western blot. Overexpression of HDAC4 resulted in only scattered senescence-associated ¦Â-galactosidase (SA-¦Â-gal) activity, which is a biomarker for senescent cells. The formation of senescence-associated heterochromatin foci (SAHF), which is another hallmar...	SIRT1	--	Knockdown//RT-PCR//Western blot//IP	We first analysed the expression patterns of SIRT1 using western blot and RT-PCR subjected to such perturbations.The protein levels of SIRT1 were markedly enhanced in HDAC4-transfected HeLa cells compared with the vector-transfected cells. In addition, we silenced HDAC4 expression in HeLa cells. Not unexpectedly, there...	--	--	--	--	Human	L	cellular senescence	26,414,199	Gene	0	0	0	0	0	0	0	0	0	1	0	1	1	0	0	1	0	0	1	0	1
ACLY	47	protein coding	HDF	--	Aging	Prevent	Cell morphological analysis//Cell proliferation assay//Knockdown//SA--gal activity assay	ACLY knockdown cells showed apparent growth retardation and a typical senescent morphology (flat and enlarged in size). The proliferation assay and senescence-associated -¦Â-galacto-sidase staining showed that knockdown of ACLY in HDF cells significantly reduced their proliferation rate. A large proportion of ACLY knoc...	--	--	--	--	p53-AMPK	--	Knockdown//SA-¦Â-gal activity assay//qRT-PCR//DAPI staining//Immunofluorescence//Pull-down assay	Initially, we silenced p53 in ACLY knockdown HDF cells, and found that additional knockdown of p53 completely abrogated ACLY silencing-induced cellular senescence. we observed an increased p53 protein level in ACLY knockdown HDF cells by confocalmicroscopy and increased mRNA levels of p53 downstream target genes by rea...	Human	L	cellular senescence	25,367,309	Gene	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0
PIR	8544	protein coding	WM266-4,IGR-37	--	Aging	Prevent	Cell morphological analysis//Colony formation assay//Knockdown//SA--gal activity assay//Western blot	The growth rate was significantly reduced in both mela-noma cell lines stably expressing shPIR constructs,compared with that of cells bearing the empty pSICO-R. A colony formation assay was also performed to measure the growth rate at low density. The number of colonies formed by shPIR cells was significantly reduced i...	--	--	--	--	--	--	--	--	Human	L	cellular senescence	21,514,450	Gene	0	0	0	1	0	0	1	0	0	0	0	1	0	0	0	1	0	0	1	0	0
CUL4B	8450	protein coding	NHF,U2OS	--	Aging	Prevent	BrdU assay//Knockdown//SA--gal activity assay//Western blot	At day 5 post exposure to 1 Gy of ionizing radiation (IR), more than 9 % of normal human fibroblasts (NHFs) became senescent, as determined by assays of senescence-associated ¦Â¨Cgalactosidase (SA- ¦Â-gal) and BrdU incorporation. At this time point, there was a remarkable reduction in CUL4B at protein level. CUL4B was...	--	--	--	--	p53-ROS	Downregulation	Knockdown//Flow cytometry//qRT-PCR//BrdU assay//SA-¦Â-gal activity assay//Western blot	We used nutlin-3, which inhibits MDM2-mediated degradation of p53 and thus stabilizes p53, to activate p53 in NHFs and measured the level of ROS. Two days after nutlin-3 treatment the intracellular ROS level was higher in NHF-shCUL4B cells than in NHF-shNeg cells . Importantly, nutlin-3 failed to elevate the ROS level ...	Human	L	cellular senescence	25,464,270	Gene	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	1	0	0
IGFBP5	3488	protein coding	HUVEC	--	Aging	Accelerate	Flow cytometry//MTT assay//RT-PCR//SA--gal activity assay//Western blot	The levels of IGFBP-5 mRNA and protein in old cells were down-regulated by gene silencing using IGFBP-5 micro-RNA lentivirus. Transduction with IGFBP-5 micro-RNA lentivirus caused 65% decrease in IGFBP-5 levels. Repression of IGFBP-5 levels in old cells caused morphological changes similar to young cells and a decrease...	p53	--	Knockdown//Western blot//MTT assay	To further confirm that the p53 activation by IGFBP-5 might be mediated through DNA damage signaling, ATM level was down-regulated using siRNAs against ATM and the effects of IGFBP-5 overexpression were measured. Increases in p53 and phospho-p53 levels induced by IGFBP-5 up-regulation were repressed by knockdown of ATM...	--	--	--	--	Human	HL	cellular senescence	17,804,819	Gene	0	0	0	0	0	0	0	0	0	1	0	0	1	1	0	1	0	0	1	0	0

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Aging ReG Dataset

Dataset Overview

Aging ReG is a manually curated database of aging factors focusing on regulatory relationships during aging with experimental evidence in humans. This dataset provides valuable insights into the molecular mechanisms of aging and the regulatory networks involved.

Key Details

Organism: Human
Description: Manually curated database of aging factors, focusing on regulatory relationships during aging with experimental evidence in human.
Source Lab: Tian lab
Reference: Piao et al., 2023
Release Date: 2023-10-24

Data Cleaning and Processing

The raw dataset was downloaded and processed to clean and organize the regulatory relationships. Data cleaning included removing duplicates, standardizing gene identifiers, and validating experimental evidence tags. The data was converted and saved in the .h5ad format to facilitate single-cell analysis workflows.

Source

The raw data was downloaded from the Aging-ReG database:
https://bio.liclab.net/Aging-ReG/download.php

This dataset contains regulatory relationships during aging with experimental evidence curated by the Tian lab. For more details, please visit the original site.

Usage

This dataset can be used for research in aging biology, bioinformatics, and related fields, especially for studying gene regulatory networks in the aging process.

Citation

If you use this dataset, please cite:
Piao et al., 2023. Raw Data : https://bio.liclab.net/Aging-ReG/download.php

Created and curated by Venkatachalam, Pooja and Albert
Date: 2025-06-14

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