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 POLR3C
Basic gene info.Gene symbolPOLR3C
Gene namepolymerase (RNA) III (DNA directed) polypeptide C (62kD)
SynonymsRPC3|RPC62
CytomapUCSC genome browser: 1q21.1
Genomic locationchr1 :145592604-145610884
Type of geneprotein-coding
RefGenesNM_006468.6,
Ensembl idENSG00000264806
DescriptionDNA-directed III 62 kDa polypeptideDNA-directed RNA polymerase III subunit CDNA-directed RNA polymerase III subunit RPC3RNA polymerase III 62 kDa subunitRNA polymerase III subunit C3
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000186141
HPRD : 17880
Vega : OTTHUMG00000013753
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_POLR3C
BioGPS: 10623
Gene Expression Atlas: ENSG00000264806
The Human Protein Atlas: ENSG00000264806
PathwayNCI Pathway Interaction Database: POLR3C
KEGG: POLR3C
REACTOME: POLR3C
ConsensusPathDB
Pathway Commons: POLR3C
MetabolismMetaCyc: POLR3C
HUMANCyc: POLR3C
RegulationEnsembl's Regulation: ENSG00000264806
miRBase: chr1 :145,592,604-145,610,884
TargetScan: NM_006468
cisRED: ENSG00000264806
ContextiHOP: POLR3C
cancer metabolism search in PubMed: POLR3C
UCL Cancer Institute: POLR3C
Assigned class in ccmGDBC

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Phenotypic Information for POLR3C(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: POLR3C
Familial Cancer Database: POLR3C
* 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: POLR3C
MedGen: POLR3C (Human Medical Genetics with Condition)
ClinVar: POLR3C
PhenotypeMGI: POLR3C (International Mouse Phenotyping Consortium)
PhenomicDB: POLR3C

Mutations for POLR3C
* 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
pancreasPOLR3Cchr1145600642145600662TXNIPchr1145441422145441442
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 POLR3C related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF335120POLR3C162551145605925145606165POLR3C2473901145606173145606316
W23948BRK1222831015745210168040POLR3C2154451145601551145606321
BI027593POLR3C11561145601562145601839POLR3C1552291145598536145598610

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 # sample1                
GAIN (# sample)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=32)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=2)
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
chr1:145608133-145608133p.Y188Y3
chr1:145594051-145594051p.R504H3
chr1:145594076-145594076p.R496C3
chr1:145608468-145608468p.N113N2
chr1:145608488-145608488p.V107I2
chr1:145608566-145608566p.R81W2
chr1:145601595-145601595p.L271I2
chr1:145592758-145592758p.E513K2
chr1:145601614-145601614p.S264S2
chr1:145601821-145601821p.A237G2

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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
# sample32 42   1  413  23 7
# mutation32 42   1  813  23 7
nonsynonymous SNV12 41   1  5 1  22 4
synonymous SNV2   1      312   1 3
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
chr1:145594051p.R504H3
chr1:145594076p.S264S2
chr1:145601614p.G232W2
chr1:145601837p.R496C2
chr1:145608142p.I491I1
chr1:145598565p.P213P1
chr1:145608189p.A469S1
chr1:145594089p.L195L1
chr1:145598609p.S464S1
chr1:145608196p.P191L1

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 POLR3C 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 POLR3C

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

ANP32E,APH1A,CHD1L,CRTC2,DAP3,GATAD2B,GPR89A,
ILF2,MRPL9,PEX11B,PI4KB,PIP5K1A,POLR3C,PRCC,
PRUNE,RBM8A,RNF115,SCNM1,SETDB1,SF3B4,VPS72
BTF3,ZFAS1,EIF3D,GNB2L1,NACA,EPB41L4A-AS1,NPM1,
POLR3C,RPL11,RPL22,RPL4,RPL5,RPL6,RPL7,
RPS18,RPS27A,RPS3A,RPS4X,RPS6,RPS7,SF3A3

ACBD6,DIEXF,C1orf43,DAP3,DEDD,MRPL9,NUP133,
NVL,POLR3C,PRUNE,RBM34,RFWD2,RNF115,RRP15,
TADA1,TBCE,TFB2M,TIPRL,TOMM20,UFC1,VPS72
C12orf10,DRG2,EIF3M,GNB2L1,PEMT,POLR3C,RNMTL1,
RPL10,RPL10A,RPL12,RPL18,RPL19,RPL30,RPL32,
RPL3,RPL7,RPL7A,RPUSD4,RSL1D1,TOMM20,WDR74
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 POLR3C


There's no related Drug.
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Cross referenced IDs for POLR3C
* 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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