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 POLR2C
Basic gene info.Gene symbolPOLR2C
Gene namepolymerase (RNA) II (DNA directed) polypeptide C, 33kDa
SynonymsRPB3|RPB31|hRPB33|hsRPB3
CytomapUCSC genome browser: 16q13-q21
Genomic locationchr16 :57496550-57505921
Type of geneprotein-coding
RefGenesNM_032940.2,
NM_002694.2,
Ensembl idENSG00000102978
DescriptionDNA-directed RNA polymerase II 33 kDa polypeptideDNA-directed RNA polymerase II subunit CDNA-directed RNA polymerase II subunit RPB3RNA polymerase II subunit 3RNA polymerase II subunit B3RPB33
Modification date20141207
dbXrefs MIM : 180663
HGNC : HGNC
Ensembl : ENSG00000102978
HPRD : 15945
Vega : OTTHUMG00000133464
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_POLR2C
BioGPS: 5432
Gene Expression Atlas: ENSG00000102978
The Human Protein Atlas: ENSG00000102978
PathwayNCI Pathway Interaction Database: POLR2C
KEGG: POLR2C
REACTOME: POLR2C
ConsensusPathDB
Pathway Commons: POLR2C
MetabolismMetaCyc: POLR2C
HUMANCyc: POLR2C
RegulationEnsembl's Regulation: ENSG00000102978
miRBase: chr16 :57,496,550-57,505,921
TargetScan: NM_032940
cisRED: ENSG00000102978
ContextiHOP: POLR2C
cancer metabolism search in PubMed: POLR2C
UCL Cancer Institute: POLR2C
Assigned class in ccmGDBC

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Phenotypic Information for POLR2C(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: POLR2C
Familial Cancer Database: POLR2C
* 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: POLR2C
MedGen: POLR2C (Human Medical Genetics with Condition)
ClinVar: POLR2C
PhenotypeMGI: POLR2C (International Mouse Phenotyping Consortium)
PhenomicDB: POLR2C

Mutations for POLR2C
* 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 POLR2C 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          
GAIN (# sample)                 
LOSS (# sample)      1          
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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=13)
Stat. for Synonymous SNVs
(# total SNVs=10)
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
chr16:57503178-57503178p.L120L2
chr16:57503193-57503194p.P125>?1
chr16:57503961-57503961p.W176C1
chr16:57496641-57496641p.P2L1
chr16:57504990-57504990p.L263V1
chr16:57503194-57503194p.R126W1
chr16:57503976-57503976p.G181G1
chr16:57499902-57499902p.V58V1
chr16:57505025-57505025p.I274I1
chr16:57503195-57503195p.R126Q1

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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
# sample2112    1  5 2  13 5
# mutation2112    1  7 2  13 5
nonsynonymous SNV2  1       4 2  12 5
synonymous SNV 111    1  3     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
chr16:57500138p.R86L2
chr16:57503178p.P2L1
chr16:57504231p.W176C1
chr16:57496641p.R86W1
chr16:57503186p.W203C1
chr16:57504902p.E207K1
chr16:57500137p.E96K1
chr16:57503195p.Y208H1
chr16:57504908p.S98S1
chr16:57503632p.S209L1

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 POLR2C 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 POLR2C

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

AARS,ARL2BP,CFAP20,CIAPIN1,COQ9,CSNK2A2,CYB5B,
DDX19B,EXOSC6,FAM192A,KATNB1,IST1,NAE1,NUDT21,
NUP93,OGFOD1,POLR2C,PSMD7,SETD6,USP10,VPS4A
CDKN2AIPNL,CNBP,CWC15,FAM162A,HAX1,KARS,MRPL40,
MRPS18B,MRPS22,MRPS7,MRPS9,NDUFA1,NDUFB4,NDUFB9,
NDUFC1,NSFL1C,POLR2C,RNF7,SRP68,TOMM7,UBB

FOPNL,CFAP20,CIAPIN1,CIRH1A,DNAJA2,DNAJA3,EXOSC5,
FAM96B,HSBP1,MRPS23,NAE1,NIP7,NUDT16L1,NUTF2,
POLR2C,POLR2G,PPP4C,PSMD7,ROMO1,PAM16,TIMM50
IFT43,OSER1,CALM2,CKLF,FIS1,GSTO1,HAX1,
LAMTOR5,LINC00493,LSM1,MYEOV2,NDUFB6,POLR2C,PSMB1,
PSMD8,PSMD9,RNF181,SELK,TRAPPC3,UBL5,ZNF410
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 POLR2C


There's no related Drug.
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Cross referenced IDs for POLR2C
* 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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