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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for POLE3 |
Basic gene info. | Gene symbol | POLE3 |
Gene name | polymerase (DNA directed), epsilon 3, accessory subunit | |
Synonyms | CHARAC17|CHRAC17|YBL1|p17 | |
Cytomap | UCSC genome browser: 9q33 | |
Genomic location | chr9 :116169517-116172955 | |
Type of gene | protein-coding | |
RefGenes | NM_001278255.1, NM_017443.4,NR_027261.1, | |
Ensembl id | ENSG00000148229 | |
Description | CHRAC-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 date | 20141207 | |
dbXrefs | MIM : 607267 | |
HGNC : HGNC | ||
Ensembl : ENSG00000148229 | ||
HPRD : 06274 | ||
Vega : OTTHUMG00000020523 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_POLE3 | |
BioGPS: 54107 | ||
Gene Expression Atlas: ENSG00000148229 | ||
The Human Protein Atlas: ENSG00000148229 | ||
Pathway | NCI Pathway Interaction Database: POLE3 | |
KEGG: POLE3 | ||
REACTOME: POLE3 | ||
ConsensusPathDB | ||
Pathway Commons: POLE3 | ||
Metabolism | MetaCyc: POLE3 | |
HUMANCyc: POLE3 | ||
Regulation | Ensembl's Regulation: ENSG00000148229 | |
miRBase: chr9 :116,169,517-116,172,955 | ||
TargetScan: NM_001278255 | ||
cisRED: ENSG00000148229 | ||
Context | iHOP: POLE3 | |
cancer metabolism search in PubMed: POLE3 | ||
UCL Cancer Institute: POLE3 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for POLE3(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: POLE3 |
Familial Cancer Database: POLE3 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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/ |
Metabolic Pathway Description | |
KEGG_PURINE_METABOLISM KEGG_PYRIMIDINE_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: POLE3 |
MedGen: POLE3 (Human Medical Genetics with Condition) | |
ClinVar: POLE3 | |
Phenotype | MGI: 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows POLE3 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
BQ020441 | POLE3 | 13 | 346 | 9 | 116169515 | 116169848 | LRRC58 | 343 | 599 | 3 | 120044647 | 120044903 | |
BF772219 | SBDS | 9 | 98 | 7 | 66458345 | 66459228 | POLE3 | 93 | 272 | 9 | 116170993 | 116171172 |
Other DBs for Structural Variants |
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Copy 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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=5) | (# total SNVs=3) |
(# total SNVs=2) | (# total SNVs=0) |
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Top 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 position | Mutation(aa) | Unique sampleID count |
chr9:116171980-116171980 | p.R61W | 2 |
chr9:116171188-116171188 | p.S116L | 2 |
chr9:116171214-116171214 | p.K107K | 1 |
chr9:116171960-116171960 | p.S67S | 1 |
chr9:116171999-116172001 | p.N54delN | 1 |
chr9:116172003-116172003 | p.N53T | 1 |
chr9:116172520-116172520 | p.I18I | 1 |
chr9:116171121-116171123 | p.E138delE | 1 |
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SNV Counts per Each Loci in TCGA data |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# 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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Top 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 Position | Mutation(aa) | Unique sampleID count |
chr9:116172003 | p.R61W,POLE3 | 1 |
chr9:116171960 | p.N53T,POLE3 | 1 |
chr9:116171980 | p.S67S,POLE3 | 1 |
Other DBs for Point Mutations |
Copy 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 |
Gene 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. |
Differential 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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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-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 |
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 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for POLE3 |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00242 | polymerase (DNA directed), epsilon 3, accessory subunit | approved; investigational | Cladribine |
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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 |
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