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 POLR2B
Basic gene info.Gene symbolPOLR2B
Gene namepolymerase (RNA) II (DNA directed) polypeptide B, 140kDa
SynonymsPOL2RB|RPB2|hRPB140|hsRPB2
CytomapUCSC genome browser: 4q12
Genomic locationchr4 :57845108-57897334
Type of geneprotein-coding
RefGenesNM_000938.1,
Ensembl idENSG00000047315
DescriptionDNA directed RNA polymerase II 140 kDa polypeptide, RNA polymerase II subunit 2, RNA polymerase II second largest subunitDNA-directed RNA polymerase II 140 kDa polypeptideDNA-directed RNA polymerase II subunit BDNA-directed RNA polymerase II subunit RP
Modification date20141207
dbXrefs MIM : 180661
HGNC : HGNC
Ensembl : ENSG00000047315
HPRD : 15943
Vega : OTTHUMG00000128771
ProteinUniProt: P30876
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_POLR2B
BioGPS: 5431
Gene Expression Atlas: ENSG00000047315
The Human Protein Atlas: ENSG00000047315
PathwayNCI Pathway Interaction Database: POLR2B
KEGG: POLR2B
REACTOME: POLR2B
ConsensusPathDB
Pathway Commons: POLR2B
MetabolismMetaCyc: POLR2B
HUMANCyc: POLR2B
RegulationEnsembl's Regulation: ENSG00000047315
miRBase: chr4 :57,845,108-57,897,334
TargetScan: NM_000938
cisRED: ENSG00000047315
ContextiHOP: POLR2B
cancer metabolism search in PubMed: POLR2B
UCL Cancer Institute: POLR2B
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for POLR2B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: POLR2B
Familial Cancer Database: POLR2B
* 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 180661; gene.
Orphanet
DiseaseKEGG Disease: POLR2B
MedGen: POLR2B (Human Medical Genetics with Condition)
ClinVar: POLR2B
PhenotypeMGI: POLR2B (International Mouse Phenotyping Consortium)
PhenomicDB: POLR2B

Mutations for POLR2B
* 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 POLR2B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
W81478POLR2B114245789694257897082IGF2BP313539272341909623419353
W81438IGF2BP3128872341909623419383POLR2B28136245789700157897082

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   4    1        
GAIN (# sample)   4    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=90)
Stat. for Synonymous SNVs
(# total SNVs=23)
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
chr4:57871762-57871762p.?5
chr4:57881715-57881715p.T616T3
chr4:57865797-57865797p.S250S3
chr4:57896476-57896476p.V1116I3
chr4:57865939-57865939p.M298L2
chr4:57891066-57891066p.K993N2
chr4:57887151-57887151p.G804S2
chr4:57861549-57861549p.V237I2
chr4:57876955-57876955p.A530A2
chr4:57877060-57877060p.?2

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample12 111 3 51 1043 188117
# mutation12 131 3 52 1243 1810123
nonsynonymous SNV11 111 2 41 843  79120
synonymous SNV 1 2  1 11 4   111 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
chr4:57896476p.S250S3
chr4:57865797p.V1116I3
chr4:57887151p.T761A2
chr4:57881683p.G804S2
chr4:57889516p.K993N2
chr4:57871515p.D846N2
chr4:57891066p.R335I2
chr4:57883852p.D606N2
chr4:57860646p.I417N1
chr4:57877199p.D617N1

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 POLR2B 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 POLR2B

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

AASDH,ANAPC1,NOA1,CEP135,CLOCK,DCUN1D4,DHX9,
EXOC1,FIP1L1,NAA15,PAICS,POLR2B,PPAT,RQCD1,
SCFD2,SLC30A6,SMARCA5,SMEK2,SRP72,USP46,XPO1
ANKRD28,CUL3,EPRS,IARS,IBTK,MED14,MIOS,
NAA35,PARG,PCM1,POLR2B,PPP2R5E,RANBP6,RQCD1,
TNKS2,TPP2,UBE3A,USP46,USP7,YME1L1,ZNF41

AASDH,ANKRD17,NOA1,CEP135,CLOCK,DCK,DHX15,
EXOC1,FIP1L1,G3BP2,GRSF1,NUP54,PAICS,POLR2B,
PPAT,SDAD1,SMARCA5,SRP72,USO1,USP46,UTP3
CDC5L,DHX36,ENOX2,FIGNL1,HAUS6,IARS,KIAA0586,
MSH6,NUDT21,NUP107,NUP155,NUP160,NUP205,PARP2,
POLA1,POLR2B,SDAD1,SKIV2L2,TOMM70A,XPO1,ZW10
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 POLR2B


There's no related Drug.
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Cross referenced IDs for POLR2B
* 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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