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 POLR3A
Basic gene info.Gene symbolPOLR3A
Gene namepolymerase (RNA) III (DNA directed) polypeptide A, 155kDa
SynonymsADDH|HLD7|RPC1|RPC155|hRPC155
CytomapUCSC genome browser: 10q22-q23
Genomic locationchr10 :79734906-79789298
Type of geneprotein-coding
RefGenesNM_007055.3,
Ensembl idENSG00000148606
DescriptionDNA-directed RNA polymerase III largest subunitDNA-directed RNA polymerase III subunit ADNA-directed RNA polymerase III subunit RPC1RNA polymerase III 155 kDa subunitRNA polymerase III subunit C1RNA polymerase III subunit C160RNA polymerase III subu
Modification date20141219
dbXrefs MIM : 614258
HGNC : HGNC
Ensembl : ENSG00000148606
HPRD : 17879
Vega : OTTHUMG00000018550
ProteinUniProt: O14802
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_POLR3A
BioGPS: 11128
Gene Expression Atlas: ENSG00000148606
The Human Protein Atlas: ENSG00000148606
PathwayNCI Pathway Interaction Database: POLR3A
KEGG: POLR3A
REACTOME: POLR3A
ConsensusPathDB
Pathway Commons: POLR3A
MetabolismMetaCyc: POLR3A
HUMANCyc: POLR3A
RegulationEnsembl's Regulation: ENSG00000148606
miRBase: chr10 :79,734,906-79,789,298
TargetScan: NM_007055
cisRED: ENSG00000148606
ContextiHOP: POLR3A
cancer metabolism search in PubMed: POLR3A
UCL Cancer Institute: POLR3A
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for POLR3A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: POLR3A
Familial Cancer Database: POLR3A
* 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
KEGG_PURINE_METABOLISM
KEGG_PYRIMIDINE_METABOLISM

check002.gifOthers
OMIM 607694; phenotype.
614258; gene.
Orphanet 77295; Odontoleukodystrophy.
88637; Hypomyelination - hypogonadotropic hypogonadism - hypodontia.
DiseaseKEGG Disease: POLR3A
MedGen: POLR3A (Human Medical Genetics with Condition)
ClinVar: POLR3A
PhenotypeMGI: POLR3A (International Mouse Phenotyping Consortium)
PhenomicDB: POLR3A

Mutations for POLR3A
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryPOLR3Achr107976134079761360DLG5chr107965733579657355
ovaryPOLR3Achr107976700279767022DLG5chr107961634079616360
pancreasPOLR3Achr107974862279748642DLG5chr107961693379616953
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows POLR3A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI193375PPM1F1210222229758622297795POLR3A202487107975080479753117

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample   2      1      
GAIN (# sample)   2      1      
LOSS (# sample)                 
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=79)
Stat. for Synonymous SNVs
(# total SNVs=33)
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
chr10:79745903-79745903p.F972L3
chr10:79762001-79762001p.L771L2
chr10:79767484-79767484p.A684P2
chr10:79777462-79777462p.Y434Y2
chr10:79769648-79769648p.R582C2
chr10:79759756-79759756p.E867*2
chr10:79739966-79739966p.A1319A2
chr10:79764506-79764506p.Q739*2
chr10:79785505-79785505p.K65E2
chr10:79778975-79778975p.P412S2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample45 16  7 62 1932  1315 13
# mutation45 17  8 62 2232  1317 12
nonsynonymous SNV43 13  6 62 1511  314 4
synonymous SNV 2 4  2    721  103 8
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
chr10:79742042p.A1210V3
chr10:79745903p.A32V2
chr10:79769648p.F972L2
chr10:79785937p.R582C2
chr10:79737257p.Y434Y1
chr10:79745855p.F1384L1
chr10:79769416p.M240I1
chr10:79782068p.Y1187F1
chr10:79741954p.Y42Y1
chr10:79753035p.G988G1

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 POLR3A 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 POLR3A

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

AP3M1,DDX21,DLG5,FAM92A1P2,FUT11,GMCL1,GTF3C3,
HSPD1,LOC650623,MAPK8,MOB4,PARG,POLR3A,RIF1,
SF3B1,TFAM,UBXN7,UPF2,VCL,WAPAL,ZMIZ1
ADNP,ANKRD17,ARID1A,CDK13,CHD6,CHD7,CHD8,
DHX33,GTF3C4,KDM3B,LMTK2,MDN1,MGA,N4BP2,
NSD1,POLR3A,TP53BP1,TRRAP,TUBGCP4,ZNF776,ZNF827

ANAPC1,AP3M1,ASXL2,DDX21,DLG5,EIF4G1,GTF3C4,
LARP1,MDN1,KMT2B___KMT2D,KAT6B,NEU3,PDCD11,POLR1A,
POLR3A,RAD54L2,RIF1,SHPRH,SNRNP200,TGFBRAP1,URB1
ANKRD17,BTAF1,FAM208B,CAD,CDK12,DDI2,IKBKAP,
ILF3,KIAA1244,LARP1,MDN1,KMT2B___KMT2D,POLR1A,POLR3A,
RBM19,RC3H2,POMK,TUBGCP4,USP24,VPRBP,ZNF142
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 POLR3A


There's no related Drug.
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Cross referenced IDs for POLR3A
* 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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