Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 POLR3K
Basic gene info.Gene symbolPOLR3K
Gene namepolymerase (RNA) III (DNA directed) polypeptide K, 12.3 kDa
SynonymsC11|C11-RNP3|RPC10|RPC11|RPC12.5
CytomapUCSC genome browser: 16p13.3
Genomic locationchr16 :96978-103632
Type of geneprotein-coding
RefGenesNM_016310.4,
Ensembl idENSG00000161980
DescriptionDNA-directed RNA polymerase III subunit KDNA-directed RNA polymerase III subunit RPC10DNA-directed RNA polymerases III 12.5 kDa polypeptideRNA polymerase III 12.5 kDa subunitRNA polymerase III subunit C10RNA polymerase III subunit C11RNA polymerase
Modification date20141207
dbXrefs MIM : 606007
HGNC : HGNC
HPRD : 16187
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_POLR3K
BioGPS: 51728
Gene Expression Atlas: ENSG00000161980
The Human Protein Atlas: ENSG00000161980
PathwayNCI Pathway Interaction Database: POLR3K
KEGG: POLR3K
REACTOME: POLR3K
ConsensusPathDB
Pathway Commons: POLR3K
MetabolismMetaCyc: POLR3K
HUMANCyc: POLR3K
RegulationEnsembl's Regulation: ENSG00000161980
miRBase: chr16 :96,978-103,632
TargetScan: NM_016310
cisRED: ENSG00000161980
ContextiHOP: POLR3K
cancer metabolism search in PubMed: POLR3K
UCL Cancer Institute: POLR3K
Assigned class in ccmGDBC

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Phenotypic Information for POLR3K(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: POLR3K
Familial Cancer Database: POLR3K
* 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
Orphanet
DiseaseKEGG Disease: POLR3K
MedGen: POLR3K (Human Medical Genetics with Condition)
ClinVar: POLR3K
PhenotypeMGI: POLR3K (International Mouse Phenotyping Consortium)
PhenomicDB: POLR3K

Mutations for POLR3K
* 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 POLR3K related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF027549POLR3K44121169705297129BLOC1S1116683125611026556113406

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=7)
Stat. for Synonymous SNVs
(# total SNVs=1)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr16:103518-103518p.F23F3
chr16:103472-103472p.?2
chr16:97554-97554p.S68L1
chr16:103474-103474p.?1
chr16:103483-103483p.T35S1
chr16:103489-103489p.N33I1
chr16:103517-103517p.S24A1
chr16:97439-97439p.W106*1
chr16:97443-97443p.R105H1
chr16:101585-101585p.A58S1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1 1       1    21  
# mutation 1 1       1    21  
nonsynonymous SNV   1       1    11  
synonymous SNV 1              1   
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
chr16:97470p.K96R1
chr16:97479p.T93I1
chr16:97531p.R76C1
chr16:97554p.S68L1
chr16:101609p.D50H1
chr16:101619p.L46L1
chr16:103518p.F23F1

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 POLR3K 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 POLR3K

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

ALG1,C16orf91,ECI1,DNAJA3,FAHD1,FLYWCH2,GFER,
HAGH,HN1L,JMJD8,MLST8,MRPS34,NDUFAB1,NDUFB10,
NPRL3,PGP,POLR3K,RAB40C,RPUSD1,SNRNP25,UBE2I
ATP6AP1,ATP6V0B,RITA1,HGH1,DCTPP1,FAM110A,LAGE3,
LOC152217,MRPL17,MRPL52,MRPS34,NABP2,PDCL3,POLR3K,
POP7,PPP1CA,RNF187,SNRPD3,STARD10,VPS25,WBSCR22

C16orf59,CMC2,CENPN,EMC8,GINS2,H2AFZ,HMOX2,
HN1L,MLST8,MRPS34,MRTO4,NDUFAB1,NUBP2,PGP,
POLR3K,PPIH,PRDX1,RANBP1,SNRNP25,TIMM10,UBE2I
ATG3,BOLA3,C1QBP,CDC123,DCAF13,HAUS1,MRPL22,
MRPL39,MRPS22,NHP2,NUP37,POLR3K,PPIH,RAN,
SLBP,SNRNP25,SNRNP40,SNRPB,SNRPD1,TAF9,UBE2T
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 POLR3K


There's no related Drug.
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Cross referenced IDs for POLR3K
* 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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