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 POLE3
Basic gene info.Gene symbolPOLE3
Gene namepolymerase (DNA directed), epsilon 3, accessory subunit
SynonymsCHARAC17|CHRAC17|YBL1|p17
CytomapUCSC genome browser: 9q33
Genomic locationchr9 :116169517-116172955
Type of geneprotein-coding
RefGenesNM_001278255.1,
NM_017443.4,NR_027261.1,
Ensembl idENSG00000148229
DescriptionCHRAC-17DNA polymerase II subunit 3DNA polymerase epsilon p17 subunitDNA polymerase epsilon subunit 3DNA polymerase epsilon subunit p17arsenic transactivated proteinarsenic-transactivated proteinasTPchromatin accessibility complex 17 kDa proteinh
Modification date20141207
dbXrefs MIM : 607267
HGNC : HGNC
Ensembl : ENSG00000148229
HPRD : 06274
Vega : OTTHUMG00000020523
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_POLE3
BioGPS: 54107
Gene Expression Atlas: ENSG00000148229
The Human Protein Atlas: ENSG00000148229
PathwayNCI Pathway Interaction Database: POLE3
KEGG: POLE3
REACTOME: POLE3
ConsensusPathDB
Pathway Commons: POLE3
MetabolismMetaCyc: POLE3
HUMANCyc: POLE3
RegulationEnsembl's Regulation: ENSG00000148229
miRBase: chr9 :116,169,517-116,172,955
TargetScan: NM_001278255
cisRED: ENSG00000148229
ContextiHOP: POLE3
cancer metabolism search in PubMed: POLE3
UCL Cancer Institute: POLE3
Assigned class in ccmGDBC

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Phenotypic Information for POLE3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: POLE3
Familial Cancer Database: POLE3
* 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: POLE3
MedGen: POLE3 (Human Medical Genetics with Condition)
ClinVar: POLE3
PhenotypeMGI: POLE3 (International Mouse Phenotyping Consortium)
PhenomicDB: POLE3

Mutations for POLE3
* 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 POLE3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ020441POLE3133469116169515116169848LRRC583435993120044647120044903
BF772219SBDS99876645834566459228POLE3932729116170993116171172

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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=5)
Stat. for Synonymous SNVs
(# total SNVs=3)
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
chr9:116171188-116171188p.S116L2
chr9:116171980-116171980p.R61W2
chr9:116171121-116171123p.E138delE1
chr9:116171214-116171214p.K107K1
chr9:116171960-116171960p.S67S1
chr9:116171999-116172001p.N54delN1
chr9:116172003-116172003p.N53T1
chr9:116172520-116172520p.I18I1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   2               1
# mutation   2               1
nonsynonymous SNV   1               1
synonymous SNV   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
chr9:116171960p.R61W,POLE31
chr9:116171980p.N53T,POLE31
chr9:116172003p.S67S,POLE31

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 POLE3 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 POLE3

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

ANP32B,FAM206A,INIP,CDCA8,EXOSC2,FANCC,HIATL1,
KIAA0368,LOC441089,MRPL50,NCBP1,NUP188,POLE3,PRPF4,
RAD23B,SET,SLC31A1,SMC2,TEX10,WDR5,ZNF367
ACP1,ATXN10,CLNS1A,COPZ1,FARSB,GTF2F2,HAT1,
LAPTM4B,MRPL3,NIF3L1,OLA1,PEX11B,PFN2,POLB,
POLE3,PPA2,PPIL1,RBBP7,SET,TXNL1,USP39

C12orf29,INIP,CKS2,EXOSC2,ISCA1,ISCA1P1,LOC441089,
LSM2,MAD2L1,MRPL50,NDUFB6,POLE3,PPIL1,PRPF4,
RMI1,RPL35,SRSF3,SNRPG,STOML2,TEX10,TRUB2
ACTL6A,ADSL,C12orf4,COA1,COMMD10,COPS3,DAP3,
DRG1,ERH,HAUS1,LSM2,MRPL49,MRPS15,MRPS23,
NHP2,NUP54,POLE3,PPP1R8,SNRNP40,TMEM126A,TOMM6
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 POLE3
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

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 3, accessory subunitapproved; investigationalCladribine


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Cross referenced IDs for POLE3
* 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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