Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for PRMT5
Basic gene info.Gene symbolPRMT5
Gene nameprotein arginine methyltransferase 5
SynonymsHRMT1L5|IBP72|JBP1|SKB1|SKB1Hs
CytomapUCSC genome browser: 14q11.2
Genomic locationchr14 :23389732-23398661
Type of geneprotein-coding
RefGenesNM_001039619.2,
NM_001282953.1,NM_001282954.1,NM_001282955.1,NM_001282956.1,
NM_006109.4,
Ensembl idENSG00000100462
Description72 kDa ICln-binding proteinHMT1 hnRNP methyltransferase-like 5SKB1 homologhistone-arginine N-methyltransferase PRMT5jak-binding protein 1protein arginine N-methyltransferase 5shk1 kinase-binding protein 1 homolog
Modification date20141222
dbXrefs MIM : 604045
HGNC : HGNC
Ensembl : ENSG00000100462
HPRD : 04955
Vega : OTTHUMG00000028709
ProteinUniProt: O14744
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PRMT5
BioGPS: 10419
Gene Expression Atlas: ENSG00000100462
The Human Protein Atlas: ENSG00000100462
PathwayNCI Pathway Interaction Database: PRMT5
KEGG: PRMT5
REACTOME: PRMT5
ConsensusPathDB
Pathway Commons: PRMT5
MetabolismMetaCyc: PRMT5
HUMANCyc: PRMT5
RegulationEnsembl's Regulation: ENSG00000100462
miRBase: chr14 :23,389,732-23,398,661
TargetScan: NM_001039619
cisRED: ENSG00000100462
ContextiHOP: PRMT5
cancer metabolism search in PubMed: PRMT5
UCL Cancer Institute: PRMT5
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PRMT5 in cancer cell metabolism1. Kanamaluru D, Xiao Z, Fang S, Choi S-E, Kim D-H, et al. (2011) Arginine methylation by PRMT5 at a naturally occurring mutation site is critical for liver metabolic regulation by small heterodimer partner. Molecular and cellular biology 31: 1540-1550. go to article

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Phenotypic Information for PRMT5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PRMT5
Familial Cancer Database: PRMT5
* This gene is included in those cancer gene databases.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_NON_CODING_RNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM 604045; gene.
604045; gene.
Orphanet
DiseaseKEGG Disease: PRMT5
MedGen: PRMT5 (Human Medical Genetics with Condition)
ClinVar: PRMT5
PhenotypeMGI: PRMT5 (International Mouse Phenotyping Consortium)
PhenomicDB: PRMT5

Mutations for PRMT5
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PRMT5 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CD696469MYL12A191361832478293253269PRMT5133624142339385923395990
BE063150PRMT5283142339140423391687PRMT577289142339413823395442
BE063240PRMT5115215142339534223395442PRMT5205469142339010623391691
DA812278PRMT51392142339166523398585DLG2393415118501346185013483

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
There's no copy number variation information in COSMIC data for this gene.

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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=38)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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check002.gifTop 10 SNVs Having the Most Samples in COSMIC data
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.
GRCh37 positionMutation(aa)Unique sampleID count
chr14:23393903-23393903p.L319V3
chr14:23395506-23395506p.?2
chr14:23393722-23393722p.R348*2
chr14:23398551-23398551p.G7V2
chr14:23391451-23391451p.?2
chr14:23393852-23393852p.Q336E2
chr14:23397790-23397790p.R49C2
chr14:23397792-23397792p.P48L2
chr14:23397352-23397352p.R100C2
chr14:23390118-23390118p.L637I1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample3417  2 3  613 252 8
# mutation3418  2 3  613 262 9
nonsynonymous SNV33 6  2 3  513 152 7
synonymous SNV 112       1   11  2
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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check002.gifTop 10 SNVs Having the Most Samples in TCGA data
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.
Genomic PositionMutation(aa)Unique sampleID count
chr14:23397792p.R83C,PRMT52
chr14:23397352p.P31Q,PRMT52
chr14:23390118p.L466I,PRMT51
chr14:23395473p.A195T,PRMT51
chr14:23393369p.H155Y,PRMT51
chr14:23394139p.A5A,PRMT51
chr14:23390166p.V450I,PRMT51
chr14:23396005p.Q165R,PRMT51
chr14:23393383p.L96M,PRMT51
chr14:23397820p.M1V,PRMT51

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for PRMT5 in TCGA
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

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Gene Expression for PRMT5

check002.gifGene Expression in Cancer Cell-lines (CCLE)
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

check002.gifDifferential Gene Expression in Primary Tumors (TCGA)
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))
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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-Expressed gene's network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

APEX1,C14orf119,NOP9,DAD1,DCAF11,HAUS4,HOMEZ,
IPO4,NGDN,OXA1L,PARP2,PRMT5,PSMB5,RBM23,
RNF31,SCAF11___GEMIN2___ZEB2,SUPT16H,THTPA,TINF2,TM9SF1,TOX4
C10orf2,DKC1,EEF1G,FBL,GLB1L2,GSTO2,HSP90AB1,
IMPDH2,IPO4,KDM1A,DANCR,NONO,PGAP2,POLR1C,
PRMT5,RAB25,RPL10A,RPS18,TMC4,TMEM177,UBIAD1

APEX1,CDCA4,CDKN3,DLGAP5,DLST,EIF2B2,EIF2S1,
FNTB,GNPNAT1,MTHFD1,PARP2,PNP,PRMT5,PSMB5,
SCAF11___GEMIN2___ZEB2,SNW1,SUPT16H,TMX1,TRMT5,VRK1,WDHD1
APEX1,CCT2,CDCA4,EBNA1BP2,EXOSC2,FARSB,GNL3,
MRPL3,NHP2L1,NOP56,NPM3,NUP35,NUP37,POLR1C,
PRMT1,PRMT5,SRP72,SUV39H2,TFDP1,UTP6,WDR77
check002.gifCo-Expressed gene's Protein-protein interaction Network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for PRMT5


There's no related Drug.
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Cross referenced IDs for PRMT5
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



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