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 POLR3F
Basic gene info.Gene symbolPOLR3F
Gene namepolymerase (RNA) III (DNA directed) polypeptide F, 39 kDa
SynonymsRPC39|RPC6
CytomapUCSC genome browser: 20p11.23
Genomic locationchr20 :18448032-18465286
Type of geneprotein-coding
RefGenesNM_001282526.1,
NM_006466.3,NR_104209.1,
Ensembl idENSG00000132664
DescriptionDNA-directed RNA polymerase III subunit RPC6RNA polymerase III C39 subunitRNA polymerase III subunit C6
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000132664
HPRD : 15156
Vega : OTTHUMG00000031971
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_POLR3F
BioGPS: 10621
Gene Expression Atlas: ENSG00000132664
The Human Protein Atlas: ENSG00000132664
PathwayNCI Pathway Interaction Database: POLR3F
KEGG: POLR3F
REACTOME: POLR3F
ConsensusPathDB
Pathway Commons: POLR3F
MetabolismMetaCyc: POLR3F
HUMANCyc: POLR3F
RegulationEnsembl's Regulation: ENSG00000132664
miRBase: chr20 :18,448,032-18,465,286
TargetScan: NM_001282526
cisRED: ENSG00000132664
ContextiHOP: POLR3F
cancer metabolism search in PubMed: POLR3F
UCL Cancer Institute: POLR3F
Assigned class in ccmGDBC

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Phenotypic Information for POLR3F(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: POLR3F
Familial Cancer Database: POLR3F
* 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: POLR3F
MedGen: POLR3F (Human Medical Genetics with Condition)
ClinVar: POLR3F
PhenotypeMGI: POLR3F (International Mouse Phenotyping Consortium)
PhenomicDB: POLR3F

Mutations for POLR3F
* 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 POLR3F related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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 1            1  
GAIN (# sample) 1            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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=12)
Stat. for Synonymous SNVs
(# total SNVs=3)
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
chr20:18464194-18464194p.E315Q4
chr20:18460797-18460797p.Q182L2
chr20:18449658-18449658p.I45V1
chr20:18462322-18462322p.K247N1
chr20:18449705-18449705p.M60I1
chr20:18462326-18462326p.E249K1
chr20:18455766-18455766p.E122*1
chr20:18462391-18462391p.Y270fs*11
chr20:18460767-18460767p.F172Y1
chr20:18462424-18462424p.G281G1

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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  13  1    1     1 2
# mutation  13  1    1     1 2
nonsynonymous SNV  12  1    1     1 2
synonymous SNV   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
chr20:18455810p.F131Y,POLR3F1
chr20:18460767p.R165I,POLR3F1
chr20:18461089p.V175V,POLR3F1
chr20:18461120p.N199H,POLR3F1
chr20:18462299p.K206N,POLR3F1
chr20:18462322p.E274K,POLR3F1
chr20:18464194p.E17K1
chr20:18448199p.I4V,POLR3F1
chr20:18449658p.I95M,POLR3F1

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 POLR3F 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 POLR3F

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

MGME1,LINC00479,CSRP2BP,DSTN,DTD1,GINS1,HAO1,
HFM1,LECT1,LOC340094,LINC00493,MATN4,NANP,LINC00112,
LINC00113,POLR3F,RBBP9,SNRPB2,SNX5,ZIC3,ZNF133
ASF1A,C10orf88,C11orf58,MZT1,C18orf32,C3orf38,TRAPPC13,
CHMP2B,DTWD1,HMGB1,JKAMP,MBIP,NUP54,PDCD10,
POLR3F,RAD17,SPAG16,TM2D1,TMEM128,UFM1,ZNF639

TMEM230,MGME1,NDUFAF5,CRLS1,CRNKL1,CSRP2BP,DTD1,
ESF1,LINC00493,MKKS,NAA20,PCNA,POLR3F,RBBP9,
SEC23B,SNRPB2,SNX5,TASP1,TRMT6,XRN2,ZNF133
ARL1,ASNSD1,BTF3L4,FAM204A,C11orf58,C12orf4,CLDND1,
COPS3,DIMT1,GPN3,LOC441089,MED21,MTMR6,NMD3,
NUDCD1,OTUD6B,PACRGL,POLR2K,POLR3F,RAD1,RCN2
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 POLR3F


There's no related Drug.
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Cross referenced IDs for POLR3F
* 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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