Browse PRDM2 in pancancer

Summary
SymbolPRDM2
NamePR/SET domain 2
Aliases RIZ; RIZ1; RIZ2; KMT8; MTB-ZF; HUMHOXY1; retinoblastoma protein-binding zinc finger protein; retinoblastoma ......
Location1p36.21
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Cancer Gene Databases ONGene (Oncogene) , TSGene (Tumor suppressor gene) , NCG (Network of Cancer Genes)
Content > Domain, Function and Classification
> Gene Ontology
> KEGG and Reactome Pathway
> Domain, Function and Classification
 
Domain PF00856 SET domain
Function

S-adenosyl-L-methionine-dependent histone methyltransferase that specifically methylates 'Lys-9' of histone H3. May function as a DNA-binding transcription factor. Binds to the macrophage-specific TPA-responsive element (MTE) of the HMOX1 (heme oxygenase 1) gene and may act as a transcriptional activator of this gene.

Classification
Class Modification Substrate Product PubMed
Histone modification write Histone methylation H3K9 H3K9me 20084102
> Gene Ontology
 
Biological Process GO:0006479 protein methylation
GO:0007568 aging
GO:0008213 protein alkylation
GO:0008340 determination of adult lifespan
GO:0010259 multicellular organism aging
GO:0016570 histone modification
GO:0016571 histone methylation
GO:0018022 peptidyl-lysine methylation
GO:0018205 peptidyl-lysine modification
GO:0032259 methylation
GO:0034968 histone lysine methylation
GO:0043414 macromolecule methylation
Molecular Function GO:0008168 methyltransferase activity
GO:0008170 N-methyltransferase activity
GO:0008276 protein methyltransferase activity
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity
GO:0016278 lysine N-methyltransferase activity
GO:0016279 protein-lysine N-methyltransferase activity
GO:0016741 transferase activity, transferring one-carbon groups
GO:0018024 histone-lysine N-methyltransferase activity
GO:0042054 histone methyltransferase activity
Cellular Component -
> KEGG and Reactome Pathway
 
KEGG hsa00310 Lysine degradation
Reactome -
Summary
SymbolPRDM2
NamePR/SET domain 2
Aliases RIZ; RIZ1; RIZ2; KMT8; MTB-ZF; HUMHOXY1; retinoblastoma protein-binding zinc finger protein; retinoblastoma ......
Location1p36.21
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Cancer Gene Databases ONGene (Oncogene) , TSGene (Tumor suppressor gene) , NCG (Network of Cancer Genes)
Content > Mutation landscape in primary tumor tissue from TCGA
> Mutation landscape in cancer cell line from CCLE
> All mutations from COSMIC database V81
> Variations from text mining
> The Cancer Genome Atlas (TCGA)
 
> Cancer Cell Line Encyclopedia (CCLE)
 
There is no record.
> Catalogue of Somatic Mutations in Cancer (COSMIC)
 
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COSMIC ID
CDS change
AA change
Mutation Type
Anatomical Site
COSM4576210c.523T>Cp.S175PSubstitution - MissenseBone
COSM1683735c.3376_3378delGTTp.V1126delVDeletion - In frameCentral_nervous_system
COSM895020c.3632G>Ap.R1211QSubstitution - MissenseEndometrium
COSM368357c.3989C>Tp.T1330ISubstitution - MissenseLung
COSM1683736c.5000_5001delAGp.E1667fs*34Deletion - FrameshiftKidney
COSM3750308c.1008G>Ap.E336ESubstitution - coding silentHaematopoietic_and_lymphoid_tissue
COSM4021538c.470C>Tp.A157VSubstitution - MissenseStomach
COSM4021560c.4194A>Tp.G1398GSubstitution - coding silentStomach
COSM1472509c.831_832insGAAp.E282_D283insEInsertion - In frameUpper_aerodigestive_tract
COSM4801918c.2158T>Cp.S720PSubstitution - MissenseLiver
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> Text Mining based Variations
 
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PMID
Variation
Cancer
Evidence
24755471MutationColorectal CarcinomaNotably, we found that exome mutation and DNA copy-number spectra in colorectal cancer cell lines closely resembled those seen in primary colorectal tumors. Similarities included the presence of two hypermutation phenotypes, as defined by signatures for defective DNA mismatch repair and DNA polymerase ε proofreading deficiency, along with concordant mutation profiles in the broadly altered WNT, MAPK, PI3K, TGFβ, and p53 pathways. Furthermore, we documented mutations enriched in genes involved in chromatin remodeling (ARID1A, CHD6, and SRCAP) and histone methylation or acetylation (ASH1L, EP300, EP400, MLL2, MLL3, PRDM2, and TRRAP).
22993552Hypermethylation; MutationCholangiocarcinomaAn understanding of the molecular mechanisms underlying the carcinogenesis and pathogenesis of CCA is necessary to improve patient survival. Therefore, we determined the genetic and epigenetic alterations of RIZ1 in 81 CCA samples and 69 matched non-tumor tissues. Methylation was found in 31 of 81 (38%) tumor samples and in 5 of 69 (7%) matched non-tumor tissues. Frameshift mutations (2 of 81) and loss of heterozygosity (LOH) (14 of 81) were not common.
16421660MutationHereditary Nonpolyposis Colorectal CancerMutations of the hMSH3, TCF4, CASP5, RIZ, RAD50, and MBD4 genes were comparatively frequent (>35 percent) in all stages.
15309726MutationGastric CarcinomaFrameshift mutations of RIZ may play an important role in gastric cancers with MSI.
14534544MutationGastric CarcinomaIn this study, we evaluated RIZ1 in 30 primary gastric cancers and found frameshift mutations in two cases (6.7%).
12082534MutationMelanomaFrameshift mutations in the RIZ gene were found in 17% of melanoma samples and 8.6% of naevi, but we could not demonstrate any missense mutations in the exons of RIZ1.
11544182Mutationdiffuse large B-cell LymphomaFinally, several missense mutations of RIZ1 were found in human tumor tissues and cell lines; one of these was particularly common in human DLBL tumors. These missense mutations, as well as the previously described frameshift mutation, all mapped to the MTase functional domains.
11135439MutationPancreatic Carcinoma; Gastric Carcinoma; Colorectal CarcinomaIn this study, we examined mutations of two poly adenine tracts, A(8) and A(9), within the coding region of the RIZ gene, in MSI-high (MSI-H) primary cancers occurring in the pancreas, stomach, and colorectum. Frameshift mutations were found in one (10%) of 10 pancreatic, four (36%) of 11 gastric, and two (25%) of eight colorectal cancers.
10987271Mutation; Loss of ExpressionGastric Carcinoma; Endometrial Carcinomaertrial carcinoma; Colorectal CarcinomaFrameshift mutations in the two coding polyadenosine tracks of RIZ were found in 19 (48%) of 40 gastric carcinomas, 6 (33%) of 18 endometrial carcinomas, 14 (26%) of 51 of colorectal carcinomas, and 7 (54%) of 13 cell lines. Eleven tumor tissues showed biallelic inactivation of RIZ.
10688904Mutation; Underexpression; Loss of ExpressionColorectal CarcinomaFour of eleven microsatellite-unstable colorectal cancer cell lines, three of which had frameshifts, showed reduced or absent mRNA expression of RIZ1.
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Summary
SymbolPRDM2
NamePR/SET domain 2
Aliases RIZ; RIZ1; RIZ2; KMT8; MTB-ZF; HUMHOXY1; retinoblastoma protein-binding zinc finger protein; retinoblastoma ......
Location1p36.21
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Cancer Gene Databases ONGene (Oncogene) , TSGene (Tumor suppressor gene) , NCG (Network of Cancer Genes)
Content > Post-translational modification (PTM)
> Post-translational modification (PTM)
 
 Filter By:
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Uniprot ID
Position
Amino Acid
Description
Upstream Enzyme
Amino Acid Sequence Variant
Q13029643SPhosphoserine-None detected
Q13029743SPhosphoserine-None detected
Q13029781SPhosphoserine-None detected
Q13029785SPhosphoserine-None detected
Q13029796SPhosphoserine-None detected
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Summary
SymbolPRDM2
NamePR/SET domain 2
Aliases RIZ; RIZ1; RIZ2; KMT8; MTB-ZF; HUMHOXY1; retinoblastoma protein-binding zinc finger protein; retinoblastoma ......
Location1p36.21
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Cancer Gene Databases ONGene (Oncogene) , TSGene (Tumor suppressor gene) , NCG (Network of Cancer Genes)
Content > Expression analysis in primary tumor tissue from TCGA
> Expression level in cancer cell line from CCLE
> Expression level in human normal tissue from HPA
> Text mining based expression change
> The Cancer Genome Atlas (TCGA)
 


  Differential expression analysis for cancers with more than 10 normal samples
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Cancer
Full Name
# N
# T
Median (N)
Median (T)
LogFC
Adj. P
Status
BLCABladder urothelial carcinoma194086.1635.73-0.5350.000157NS
BRCABreast invasive carcinoma11211006.4616.017-0.474.77e-18NS
CESCCervical and endocervical cancers33066.075.576NANANA
COADColon adenocarcinoma414595.5865.305-0.3440.000136NS
ESCAEsophageal carcinoma111856.4535.99-0.4720.0172NS
GBMGlioblastoma multiforme51667.1955.338NANANA
HNSCHead and Neck squamous cell carcinoma445225.955.554-0.4311.8e-06NS
KIRCKidney renal clear cell carcinoma725345.6595.216-0.4931.07e-17NS
KIRPKidney renal papillary cell carcinoma322915.4554.829-0.5898.78e-08Under
LAMLAcute Myeloid Leukemia0173NA7.36NANANA
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> Cancer Cell Line Encyclopedia (CCLE)
 



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Tissue
Cell Line
Expression Level (Microarray)
Autonomic gangliaCHP1266
Autonomic gangliaCHP2125.9
Autonomic gangliaIMR326.1
Autonomic gangliaKELLY6.9
Autonomic gangliaKPNRTBM16.2
Autonomic gangliaKPNSI9S5.5
Autonomic gangliaKPNYN6.1
Autonomic gangliaMHHNB116.2
Autonomic gangliaNB16.3
Autonomic gangliaNH66
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> The Human Protein Atlas (HPA)
 


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Tissue
Expression Level (TPM)
Adipose tissue18.3
Adrenal gland19.1
Appendix26.8
Bone marrow51.3
Breast21.9
Cerebral cortex44.4
Cervix, uterine24
Colon12.6
Duodenum13.4
Endometrium30.1
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> Text Mining based Expression
 
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PMID
Expression
Cancer
Evidence
28339081underexpression (hypermethylation)Hepatocellular CarcinomaRIZ1 gene, a candidate HCC suppressor gene, is frequently found to be hypermethylated and downregulated in HCC.
26690953UnderexpressionGliomaReal-time polymerase chain reaction and western blot analysis showed that RIZ1 was downregulated in high-grade gliomas compared with low-grade gliomas and normal brain tissue.
25987089Underexpression (hypermethylation); Loss of ExpressionRenal Cell CarcinomaRIZ1 expression was down-regulated or lost in OS-RC-2, 769-P, Caki-1, 786-O and A498 RCC cell lines. RIZ1 expression is down-regulated in human RCC, and this down-regulation is associated with methylation.
25722013altered expressionParathyroid Gland NeoplasmImpaired expression of the histone methyltransferases EZH2, BMI1, and RIZ1 have been described in parathyroid tumors.
24966940Underexpression (hypermethylation)Lung CarcinomaPRDM2, PRDM5, PRDM16 promoters are methylated and their expression is suppressed in lung cancer cells.
24441146Overexpressionpediatric Myeloid LeukemiaGene expression profiling showed a unique signature characterized by significantly higher expression of EYA3, SESN1, PRDM2/RIZ, and HIST2H4 genes. In conclusion, t(6;9)/DEK-NUP214 represents a unique subtype of acute myeloid leukemia with a high risk of relapse, high frequency of FLT3-ITD, and a specific gene expression signature.
24040155altered expressionRectal cacinomaTwenty seven out of 35 patients were finally included in the study. We performed a multiple t-test using Significance Analysis of Microarrays, to find those genes differing significantly in expression, between responders (n=11) and non-responders (n=16) to CRT. The differently expressed genes were: BC 035656.1, CIR, PRDM2, CAPG, FALZ, HLA-DPB2, NUPL2, and ZFP36.
22614009UnderexpressionMalignant meningiomaThese results from our study indicate that RIZ1 expression is significantly downregulated as the formation of meningiomas progressed, and suggest that RIZ1 may represent a promising candidate tumor suppressor gene that contributes to malignant meningiomas.
22372344Underexpression (hypermethylation)Esophageal Squamous Cell CarcinomaIn the 28 ESCC patient samples, RIZ1 expression was significantly lower in the tumor tissues than that in their adjacent non-cancerous tissues (p < 0.05). Methylation of the RIZ1 promoter and loss of RIZ1 expression in human ESCC are independent biomarkers.
22363126Underexpression (hypermethylation)Esophageal Squamous Cell CarcinomaThe expression of RIZ1 mRNA in TE-13 was up-regulated after treatment with 5-aza-CdR. Promoter methylation may play an important role in the epigenetic silencing of RIZ1 gene expression in human ESCC.
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Summary
SymbolPRDM2
NamePR/SET domain 2
Aliases RIZ; RIZ1; RIZ2; KMT8; MTB-ZF; HUMHOXY1; retinoblastoma protein-binding zinc finger protein; retinoblastoma ......
Location1p36.21
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Cancer Gene Databases ONGene (Oncogene) , TSGene (Tumor suppressor gene) , NCG (Network of Cancer Genes)
Content > Somatic copy number alteration in primary tomur tissue
> The Cancer Genome Atlas (TCGA)
 


  Correlation between expression and SCNA as well as percentage of patients in different status.
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Cancer
Full Name
# Sample
R
P
% Loss
% Neutral
% Gain
Status
BLCABladder urothelial carcinoma4040.4337.3e-2018.361.420.3Neutral
BRCABreast invasive carcinoma10750.4773.8e-6241.852.75.6Loss
CESCCervical and endocervical cancers2920.5219.81e-2212.759.927.4Neutral
COADColon adenocarcinoma4490.3678.43e-1633.963.72.4Loss
ESCAEsophageal carcinoma1830.4834.54e-123547.517.5Loss
GBMGlioblastoma multiforme1470.5524.04e-1310.270.719Neutral
HNSCHead and Neck squamous cell carcinoma5140.4093.43e-2218.170.811.1Neutral
KIRCKidney renal clear cell carcinoma5250.3021.49e-1218.9801.1Neutral
KIRPKidney renal papillary cell carcinoma2880.5092e-2018.181.20.7Neutral
LAMLAcute Myeloid Leukemia1660.0530.4990.6972.4Neutral
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Summary
SymbolPRDM2
NamePR/SET domain 2
Aliases RIZ; RIZ1; RIZ2; KMT8; MTB-ZF; HUMHOXY1; retinoblastoma protein-binding zinc finger protein; retinoblastoma ......
Location1p36.21
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Cancer Gene Databases ONGene (Oncogene) , TSGene (Tumor suppressor gene) , NCG (Network of Cancer Genes)
Content > Methylation level in the promoter region of CR
> Methylation level in the promoter region of CR
 


  Correlation between expression and methylation as well as differential methylation analysis.
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Cancer
Full Name
R
P
# N
# T
Delta beta (T vs N)
P value (T vs N)
Status
BLCABladder urothelial carcinoma-0.3741.36e-1517408-0.1340.00288NS/NA
BRCABreast invasive carcinoma-0.3420837850.0046.31e-09NS/NA
CESCCervical and endocervical cancers-0.3512.99e-103306NANANS/NA
COADColon adenocarcinoma-0.3492.37e-10192970.0010.0199NS/NA
ESCAEsophageal carcinoma-0.48109185NANANS/NA
GBMGlioblastoma multiforme-0.4845.43e-05164NANANS/NA
HNSCHead and Neck squamous cell carcinoma-0.2654.24e-10205220.0020.00294NS/NA
KIRCKidney renal clear cell carcinoma-0.3031.17e-08243190.2275.82e-08Increased
KIRPKidney renal papillary cell carcinoma-0.3621.67e-10232750.0030.0545NS/NA
LAMLAcute Myeloid Leukemia-0.3872.28e-070170NANANS/NA
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Summary
SymbolPRDM2
NamePR/SET domain 2
Aliases RIZ; RIZ1; RIZ2; KMT8; MTB-ZF; HUMHOXY1; retinoblastoma protein-binding zinc finger protein; retinoblastoma ......
Location1p36.21
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Cancer Gene Databases ONGene (Oncogene) , TSGene (Tumor suppressor gene) , NCG (Network of Cancer Genes)
Content > Primary tumor tissue from TCGA
> Normal tumor tissue from HPA
>The Cancer Genome Atlas (TCGA)
 
There is no record.
> The Human Protein Atlas (HPA)
 


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Tissue
Level
Level Name
Adrenal gland2Medium
Appendix1Low
Bone marrow1Low
Breast2Medium
Bronchus1Low
Caudate3High
Cerebellum2Medium
Cerebral cortex3High
Cervix, uterine1Low
Colon1Low
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Summary
SymbolPRDM2
NamePR/SET domain 2
Aliases RIZ; RIZ1; RIZ2; KMT8; MTB-ZF; HUMHOXY1; retinoblastoma protein-binding zinc finger protein; retinoblastoma ......
Location1p36.21
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Cancer Gene Databases ONGene (Oncogene) , TSGene (Tumor suppressor gene) , NCG (Network of Cancer Genes)
Content > Association between expresson and subtype
> Overall survival analysis based on expression
> Association between expresson and stage
> Association between expresson and grade
> Subtype
 


  Association between expresson and subtype.
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Cancer
Full Name
# Patients
P Value (Kruskal-Wallis)
Association
Source
BLCABladder urothelial carcinoma1280.704NS24476821
BRCABreast invasive carcinoma5214.31e-05Significant23000897
COADColon adenocarcinoma1490.000995Significant22810696
GBMGlioblastoma multiforme1570.0215Significant26824661
HNSCHead and Neck squamous cell carcinoma2793.57e-06Significant25631445
KIRPKidney renal papillary cell carcinoma1610.0194Significant26536169
LGGBrain Lower Grade Glioma5132.42e-30Significant26824661
LUADLung adenocarcinoma2301.95e-05Significant25079552
LUSCLung squamous cell carcinoma1780.336NS22960745
OVOvarian serous cystadenocarcinoma2870.0399Significant21720365
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> Overall survival
 

  Overall survival analysis based on expression.
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Cancer
Full Name
# Patients
Hazard Ratio
P Value (Log Rank Test)
Association
BLCABladder urothelial carcinoma405 0.7240.131NS
BRCABreast invasive carcinoma1079 1.1190.621NS
CESCCervical and endocervical cancers291 1.4360.289NS
COADColon adenocarcinoma439 0.9870.968NS
ESCAEsophageal carcinoma184 0.6690.242NS
GBMGlioblastoma multiforme158 0.8840.624NS
HNSCHead and Neck squamous cell carcinoma518 0.560.00271Longer
KIRCKidney renal clear cell carcinoma531 0.930.745NS
KIRPKidney renal papillary cell carcinoma287 0.2990.0146Longer
LAMLAcute Myeloid Leukemia149 1.0320.892NS
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> Stage
 

  Association between expresson and stage.
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Cancer
Full Name
# Patients
R Value (Spearman)
P Value (Spearman)
Association
BLCABladder urothelial carcinoma406 -0.0570.256NS
BRCABreast invasive carcinoma1071 -0.0580.0564NS
CESCCervical and endocervical cancers167 0.0060.934NS
COADColon adenocarcinoma445 -0.0060.895NS
ESCAEsophageal carcinoma162 -0.0260.741NS
HNSCHead and Neck squamous cell carcinoma448 -0.0620.192NS
KIRCKidney renal clear cell carcinoma531 -0.0710.104NS
KIRPKidney renal papillary cell carcinoma260 -0.2475.8e-05Lower
LIHCLiver hepatocellular carcinoma347 0.0860.109NS
LUADLung adenocarcinoma507 -0.1410.00149Lower
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> Grade
 

  Association between expresson and grade.
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Cancer
Full Name
# Patients
R Value (Spearman)
P Value (Spearman)
Association
CESCCervical and endocervical cancers272 -0.1150.0578NS
HNSCHead and Neck squamous cell carcinoma498 0.0010.98NS
KIRCKidney renal clear cell carcinoma525 -0.0640.141NS
LGGBrain Lower Grade Glioma514 -0.030.49NS
LIHCLiver hepatocellular carcinoma366 -0.0530.313NS
OVOvarian serous cystadenocarcinoma296 -0.0750.198NS
PAADPancreatic adenocarcinoma176 -0.0220.774NS
STADStomach adenocarcinoma406 0.1140.0214Higher
UCECUterine Corpus Endometrial Carcinoma534 0.1180.00654Higher
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Summary
SymbolPRDM2
NamePR/SET domain 2
Aliases RIZ; RIZ1; RIZ2; KMT8; MTB-ZF; HUMHOXY1; retinoblastoma protein-binding zinc finger protein; retinoblastoma ......
Location1p36.21
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Cancer Gene Databases ONGene (Oncogene) , TSGene (Tumor suppressor gene) , NCG (Network of Cancer Genes)
Content > Targets inferred by reverse engineering method
> Targets identified by ChIP-seq data
> Targets inferred by reverse engineering method
 
> Targets identified by ChIP-seq data
 
Summary
SymbolPRDM2
NamePR/SET domain 2
Aliases RIZ; RIZ1; RIZ2; KMT8; MTB-ZF; HUMHOXY1; retinoblastoma protein-binding zinc finger protein; retinoblastoma ......
Location1p36.21
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Cancer Gene Databases ONGene (Oncogene) , TSGene (Tumor suppressor gene) , NCG (Network of Cancer Genes)
Content > Drugs from DrugBank database
> Drugs from DrugBank database
 
There is no record for PRDM2.
Summary
SymbolPRDM2
NamePR/SET domain 2
Aliases RIZ; RIZ1; RIZ2; KMT8; MTB-ZF; HUMHOXY1; retinoblastoma protein-binding zinc finger protein; retinoblastoma ......
Location1p36.21
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Cancer Gene Databases ONGene (Oncogene) , TSGene (Tumor suppressor gene) , NCG (Network of Cancer Genes)
Content > Protein-Protein Interaction Network
> miRNA Regulatory Relationship
> Interactions from Text Mining
> Protein-Protein Interaction Network
 
> miRNA Regulatory Relationship
 
> Interactions from Text Mining
 
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PMID
Cancer
Hierarchy
Gene
Relation to CR
Evidence
28339081Hepatocellular CarcinomaupstreamDNMT1; HBxnegative regulationHBx recombinant transfection increased DNMT1 expression level and suppressed RIZ1 expression. Moreover, knockdown of DNMT1 by siRNA restored RIZ1 expression in HCC cell SMMC-7721 and reduced methylated CpG sites of RIZ1.
26690953GliomapartnerKi-67Negative correlationThere was a negative correlation between RIZ1 and Ki-67 immunoreactivity.
22614009Malignant meningiomapartnerc-mycNegative correlationFurthermore, RIZ1 overexpression in malignant meningioma cells was associated with the downregulation of c-myc expression.
17963297Hepatocellular CarcinomapartnerSMYD3Negative correlationSMYD3 over-expression in HCC was associated with RIZ1 hypermethylation and mRNA down-expression.
17052263Prostate Carcinomapartnerp53AssociationAll four PCa specimens with nuclear accumulation of p53 were stage III disease and showed DNA methylation of RIZ1.
10688904Colorectal Carcinomaupstreamp1RegulationWe propose that RIZ is a target of the observed 1p alterations, with impairment of the PR domain-mediated function through either frameshift mutation or genomic deletion.
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