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 POLR2A
Basic gene info.Gene symbolPOLR2A
Gene namepolymerase (RNA) II (DNA directed) polypeptide A, 220kDa
SynonymsPOLR2|POLRA|RPB1|RPBh1|RPO2|RPOL2|RpIILS|hRPB220|hsRPB1
CytomapUCSC genome browser: 17p13.1
Genomic locationchr17 :7387697-7417935
Type of geneprotein-coding
RefGenesNM_000937.4,
Ensembl idENSG00000181222
DescriptionDNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunitDNA-directed RNA polymerase II subunit ADNA-directed RNA polymerase II subunit RPB1DNA-directed RNA polymerase III largest subunitRNA polymerase II subunit B1RNA-directed
Modification date20141207
dbXrefs MIM : 180660
HGNC : HGNC
Ensembl : ENSG00000181222
HPRD : 08916
Vega : OTTHUMG00000177594
ProteinUniProt: P24928
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_POLR2A
BioGPS: 5430
Gene Expression Atlas: ENSG00000181222
The Human Protein Atlas: ENSG00000181222
PathwayNCI Pathway Interaction Database: POLR2A
KEGG: POLR2A
REACTOME: POLR2A
ConsensusPathDB
Pathway Commons: POLR2A
MetabolismMetaCyc: POLR2A
HUMANCyc: POLR2A
RegulationEnsembl's Regulation: ENSG00000181222
miRBase: chr17 :7,387,697-7,417,935
TargetScan: NM_000937
cisRED: ENSG00000181222
ContextiHOP: POLR2A
cancer metabolism search in PubMed: POLR2A
UCL Cancer Institute: POLR2A
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for POLR2A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: POLR2A
Familial Cancer Database: POLR2A
* 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 180660; gene+phenotype.
Orphanet
DiseaseKEGG Disease: POLR2A
MedGen: POLR2A (Human Medical Genetics with Condition)
ClinVar: POLR2A
PhenotypeMGI: POLR2A (International Mouse Phenotyping Consortium)
PhenomicDB: POLR2A

Mutations for POLR2A
* 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
pancreasPOLR2Achr1774126567412676ZBTB4chr1773838997383919
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 POLR2A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE819347NUP18831519131768587131768868POLR2A1382871774070227411630
BF805544CEP2501236203409264234095612POLR2A2305381774166117416919
DA107051GPM6A12484176622745176733415POLR2A2495811774041387404883
BI061851IKZF1116275042479150424953POLR2A1513441774043787404893
BF514571POLR2A18791774007677400828POLR2A742851774010127401430
BF512093POLR2A18791774007677400828POLR2A742851774010127401430
BI059477IKZF1116275042479150424953POLR2A1513441774043787404893
BE833427USP12528132766606127666087POLR2A182581774161287416459
BE819348NUP188131769131768570131768868POLR2A1633121774070227411630
BI022194AP2B11211173395159133953833POLR2A2034371774039727404297
BE159844POLR2A39601774092317409252PVRL245382194537669445377031

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)   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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=108)
Stat. for Synonymous SNVs
(# total SNVs=48)
Stat. for Deletions
(# total SNVs=6)
Stat. for Insertions
(# total SNVs=1)

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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
chr17:7416599-7416599p.S1672S4
chr17:7412911-7412911p.R1258H3
chr17:7399866-7399866p.G157G3
chr17:7405316-7405316p.G816V3
chr17:7401440-7401440p.A416T3
chr17:7405418-7405418p.T850K2
chr17:7417385-7417385p.S1934S2
chr17:7400127-7400127p.S194S2
chr17:7416926-7416926p.P1781P2
chr17:7416391-7416391p.R1603H2

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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
# sample 51172 11 72 14411 1818116
# mutation 51172 11 72 15411 2222128
nonsynonymous SNV 4 111 9 62 103 1 1317120
synonymous SNV 1161 2 1  511  95 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
chr17:7399844p.G150D3
chr17:7401440p.A416T3
chr17:7404318p.C451C2
chr17:7416821p.T647T2
chr17:7402375p.R475H2
chr17:7416391p.P1746P2
chr17:7402446p.L1956L2
chr17:7417451p.R1603H2
chr17:7414879p.F1041V1
chr17:7417116p.L1382L1

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 POLR2A 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 POLR2A

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

ANKFY1,ANKHD1-EIF4EBP3,ARID1A,BAZ2A,BCOR,CTC1,C9orf129,
CYB5D1,DNAJC16,FRY,GIGYF2,HEATR5B,KDM3B,NCOR1,
POLR2A,PRPF8,RABEP1,SPG11,THRAP3,TP53BP1,ZBTB4
ARID1A,BRPF3,C2CD3,COL4A5,EP400,KIAA0556,KIAA1217,
KIAA1549,MAML1,MAP3K9,MDC1,POLR2A,SIPA1L1,SIPA1L3,
SRCAP,TRRAP,TTLL5,YLPM1,ZNF135,ZNF142,ZSWIM5

ALKBH5,ANKFY1,ARID1A,C17orf85,CAMTA2,FLII,FXR2,
KDM6B,NCOR1,PAFAH1B1,POLR2A,PRPF8,RABEP1,RAI1,
SMG6,THRAP3,TNRC6B,TOP3A,WDR7,ZCCHC2,ZNF407
ACIN1,ANKRD52,BAZ2A,EP300,GBF1,GOLGA3,GTF3C1,
HTT,KDM2A,KIAA2018,KMT2B___KMT2D,MYH9,NCOA6,PCNT,
POLR2A,SMARCA4,SPEN,SRCAP,TCF20,TRRAP,UBR4
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 POLR2A
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P24928; -.
ChemistryChEMBL CHEMBL1641353; -.
Organism-specific databasesPharmGKB PA33507; -.
Organism-specific databasesCTD 5430; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00269polymerase (RNA) II (DNA directed) polypeptide A, 220kDaapprovedChlorotrianisene
DB00286polymerase (RNA) II (DNA directed) polypeptide A, 220kDaapprovedConjugated Estrogens
DB00255polymerase (RNA) II (DNA directed) polypeptide A, 220kDaapprovedDiethylstilbestrol
DB00783polymerase (RNA) II (DNA directed) polypeptide A, 220kDaapproved; investigationalEstradiol
DB00655polymerase (RNA) II (DNA directed) polypeptide A, 220kDaapprovedEstrone
DB00977polymerase (RNA) II (DNA directed) polypeptide A, 220kDaapprovedEthinyl Estradiol
DB00890polymerase (RNA) II (DNA directed) polypeptide A, 220kDaapprovedDienestrol
DB00675polymerase (RNA) II (DNA directed) polypeptide A, 220kDaapprovedTamoxifen
DB00394polymerase (RNA) II (DNA directed) polypeptide A, 220kDaapprovedBeclomethasone
DB00443polymerase (RNA) II (DNA directed) polypeptide A, 220kDaapprovedBetamethasone
DB01222polymerase (RNA) II (DNA directed) polypeptide A, 220kDaapproved; investigationalBudesonide
DB01410polymerase (RNA) II (DNA directed) polypeptide A, 220kDaapproved; investigationalCiclesonide
DB01260polymerase (RNA) II (DNA directed) polypeptide A, 220kDaapproved; investigationalDesonide
DB01234polymerase (RNA) II (DNA directed) polypeptide A, 220kDaapproved; investigationalDexamethasone
DB00180polymerase (RNA) II (DNA directed) polypeptide A, 220kDaapproved; investigationalFlunisolide
DB00588polymerase (RNA) II (DNA directed) polypeptide A, 220kDaapproved; investigationalFluticasone Propionate
DB00741polymerase (RNA) II (DNA directed) polypeptide A, 220kDaapprovedHydrocortisone
DB00959polymerase (RNA) II (DNA directed) polypeptide A, 220kDaapprovedMethylprednisolone
DB00764polymerase (RNA) II (DNA directed) polypeptide A, 220kDaapprovedMometasone
DB01384polymerase (RNA) II (DNA directed) polypeptide A, 220kDaapprovedParamethasone
DB00860polymerase (RNA) II (DNA directed) polypeptide A, 220kDaapprovedPrednisolone
DB00635polymerase (RNA) II (DNA directed) polypeptide A, 220kDaapprovedPrednisone
DB00896polymerase (RNA) II (DNA directed) polypeptide A, 220kDaapprovedRimexolone
DB00620polymerase (RNA) II (DNA directed) polypeptide A, 220kDaapprovedTriamcinolone


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Cross referenced IDs for POLR2A
* 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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