Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 POLE
Basic gene info.Gene symbolPOLE
Gene namepolymerase (DNA directed), epsilon, catalytic subunit
SynonymsCRCS12|FILS|POLE1
CytomapUCSC genome browser: 12q24.3
Genomic locationchr12 :133200347-133263945
Type of geneprotein-coding
RefGenesNM_006231.3,
Ensembl idENSG00000177084
DescriptionDNA polymerase II subunit ADNA polymerase epsilon catalytic subunit A
Modification date20141207
dbXrefs MIM : 174762
HGNC : HGNC
Ensembl : ENSG00000177084
HPRD : 07177
Vega : OTTHUMG00000168045
ProteinUniProt: Q07864
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_POLE
BioGPS: 5426
Gene Expression Atlas: ENSG00000177084
The Human Protein Atlas: ENSG00000177084
PathwayNCI Pathway Interaction Database: POLE
KEGG: POLE
REACTOME: POLE
ConsensusPathDB
Pathway Commons: POLE
MetabolismMetaCyc: POLE
HUMANCyc: POLE
RegulationEnsembl's Regulation: ENSG00000177084
miRBase: chr12 :133,200,347-133,263,945
TargetScan: NM_006231
cisRED: ENSG00000177084
ContextiHOP: POLE
cancer metabolism search in PubMed: POLE
UCL Cancer Institute: POLE
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for POLE(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: POLE
Familial Cancer Database: POLE
* 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 UCEC 6,

Therapeutic Vulnerabilities in Cancer7

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,
6 http://www.nature.com/nature/journal/v497/n7447/full/nature12113.html,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
KEGG_PURINE_METABOLISM
KEGG_PYRIMIDINE_METABOLISM

check002.gifOthers
OMIM 174762; gene.
615083; phenotype.
615139; phenotype.
Orphanet 352712; Facial dysmorphism - immunodeficiency - livedo - short stature.
DiseaseKEGG Disease: POLE
MedGen: POLE (Human Medical Genetics with Condition)
ClinVar: POLE
PhenotypeMGI: POLE (International Mouse Phenotyping Consortium)
PhenomicDB: POLE

Mutations for POLE
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryPOLEchr12133202263133202283chr125975977159759791
ovaryPOLEchr12133259196133259216PGAM5chr12133287796133287816
pancreasPOLEchr12133219226133219246POLEchr12133219321133219341
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 POLE related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AB209902POLE1357612133225513133254307HMGCL3572506712412837724147086
BG986284POLE318112133208986133209317ADM177321111032841110328555

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
There's no copy number variation information in COSMIC data for this gene.

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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=16

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=190)
Stat. for Synonymous SNVs
(# total SNVs=46)
Stat. for Deletions
(# total SNVs=4)
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
chr12:133253184-133253184p.P286R15
chr12:133250289-133250289p.V411L9
chr12:133220532-133220532p.V1394A4
chr12:133244137-133244137p.T757T3
chr12:133250250-133250250p.L424I3
chr12:133245305-133245305p.E648K2
chr12:133214671-133214671p.N1869N2
chr12:133249237-133249237p.S554S2
chr12:133219579-133219579p.R1519C2
chr12:133226355-133226355p.L1235I2

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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=10

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample69 35  8 3  2393 12220231
# mutation79 37  9 3  3293 12327249
nonsynonymous SNV67 31  6 3  2662  1219135
synonymous SNV12 7  3    631 1118114
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
chr12:133253184p.P286H10
chr12:133250289p.V411L8
chr12:133220532p.V1394A4
chr12:133250250p.S297F3
chr12:133253151p.L424V3
chr12:133248877p.A1967V2
chr12:133214643p.S459F2
chr12:133249847p.R1308R2
chr12:133225973p.G1425G2
chr12:133214671p.R1111Q2

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 POLE 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 POLE

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

ANAPC11,AP2S1,C19orf24,C19orf70,CHCHD5,COMMD4,FDX1L,
GADD45GIP1,JOSD2,MRPL53,LINC00116,NDUFA11,NDUFA13,NDUFB2,
NDUFB7,POLE4,RNF181,RPS19BP1,TIMM13,TMEM160,UQCR11
ATP5E,ATP6V0E1,ATP6V1F,MINOS1,BRK1,CAPNS1,DYNLRB1,
KRTCAP2,MGST2,NEDD8,NOP10,OST4,PKIG,POLE4,
RBX1,RNASEK,RNF181,SERF2,SRP14,TAF10,VKORC1

ANAPC11,UQCC3,ATRAID,PTRHD1,C7orf55,DTYMK,ISCA2,
MRPL11,MRPS28,MYEOV2,LINC00116,NDUFB1,NDUFB2,NDUFB7,
OST4,POLE4,SIVA1,STRA13,PAM16,TIMM8B,UQCR11
ATP5O,BUD31,COX14,CAPZA2,COMMD3,FIS1,GOLGA7,
NDUFA11,NDUFA13,NDUFA8,NDUFB7,NDUFS4,NFU1,PEX2,
POLE4,SRP14,SUPT4H1,TMEM14C,TRAPPC3,UQCR11,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 POLE
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryChEMBL CHEMBL2363042; -.
Organism-specific databasesPharmGKB PA277; -.
Organism-specific databasesCTD 5426; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00242polymerase (DNA directed), epsilon, catalytic subunitapproved; investigationalCladribine
DB01033polymerase (DNA directed), epsilon, catalytic subunitapprovedMercaptopurine
DB00563polymerase (DNA directed), epsilon, catalytic subunitapprovedMethotrexate
DB00441polymerase (DNA directed), epsilon, catalytic subunitapprovedGemcitabine


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Cross referenced IDs for POLE
* 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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