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 POLD3
Basic gene info.Gene symbolPOLD3
Gene namepolymerase (DNA-directed), delta 3, accessory subunit
SynonymsP66|P68|PPP1R128
CytomapUCSC genome browser: 11q14
Genomic locationchr11 :74303649-74354105
Type of geneprotein-coding
RefGenesNM_006591.2,
NR_046409.1,NR_046410.1,
Ensembl idENSG00000077514
DescriptionDNA polymerase delta subunit 3DNA polymerase delta subunit p66Pol delta C subunit (p66)protein phosphatase 1, regulatory subunit 128
Modification date20141207
dbXrefs MIM : 611415
HGNC : HGNC
Ensembl : ENSG00000077514
HPRD : 11446
Vega : OTTHUMG00000165621
ProteinUniProt: Q15054
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_POLD3
BioGPS: 10714
Gene Expression Atlas: ENSG00000077514
The Human Protein Atlas: ENSG00000077514
PathwayNCI Pathway Interaction Database: POLD3
KEGG: POLD3
REACTOME: POLD3
ConsensusPathDB
Pathway Commons: POLD3
MetabolismMetaCyc: POLD3
HUMANCyc: POLD3
RegulationEnsembl's Regulation: ENSG00000077514
miRBase: chr11 :74,303,649-74,354,105
TargetScan: NM_006591
cisRED: ENSG00000077514
ContextiHOP: POLD3
cancer metabolism search in PubMed: POLD3
UCL Cancer Institute: POLD3
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of POLD3 in cancer cell metabolism1. Bursomanno S, Beli P, Khan AM, Minocherhomji S, Wagner SA, et al. (2015) Proteome-wide analysis of SUMO2 targets in response to pathological DNA replication stress in human cells. DNA repair 25: 84-96. go to article

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Phenotypic Information for POLD3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: POLD3
Familial Cancer Database: POLD3
* 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 611415; gene.
Orphanet
DiseaseKEGG Disease: POLD3
MedGen: POLD3 (Human Medical Genetics with Condition)
ClinVar: POLD3
PhenotypeMGI: POLD3 (International Mouse Phenotyping Consortium)
PhenomicDB: POLD3

Mutations for POLD3
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
ovaryPOLD3chr117431458974314609POLD3chr117431466974314689
ovaryPOLD3chr117431748574317505POLD3chr117431756174317581
ovaryPOLD3chr117431816674318186CHUKchr10101986201101986221
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 POLD3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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        3 1   1  
GAIN (# sample)        3 1   1  
LOSS (# sample)        1        
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=7

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=27)
Stat. for Synonymous SNVs
(# total SNVs=12)
Stat. for Deletions
(# total SNVs=5)
Stat. for Insertions
(# total SNVs=2)

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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
chr11:74347268-74347268p.K382K4
chr11:74336609-74336609p.R300fs*54
chr11:74329615-74329615p.P142P3
chr11:74347267-74347267p.K382R3
chr11:74336498-74336498p.I262fs*12
chr11:74347270-74347270p.R383Q2
chr11:74347275-74347275p.R385G2
chr11:74329805-74329805p.E206*2
chr11:74336608-74336609p.R300fs*92
chr11:74329822-74329822p.T211T2

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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=7

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample3  12  3    212  61 5
# mutation3  7  3    322  62 5
nonsynonymous SNV3  5  3    311  22 4
synonymous SNV   2        11  4  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
chr11:74347268p.K382K4
chr11:74347267p.K382R3
chr11:74347275p.R385C2
chr11:74329822p.T211T2
chr11:74331075p.P327R1
chr11:74323962p.A106A1
chr11:74331108p.D330H1
chr11:74347270p.F115F1
chr11:74323981p.V372I1
chr11:74336521p.P142H1

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 POLD3 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 POLD3

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

ACER3,AQP11,ARHGEF17,C11orf30,ZNF436-AS1,C2CD3,CAPN5,
KLHL35,LIPT2,LOC653566,NEU3,OMP,PAK1,POLD3,
PPME1,PRKRIR,RNF169,SPCS2,USP35,UVRAG,XRRA1
MIS18BP1,CTDSPL2,EPC2,ZC2HC1A,HMGXB4,CEP162,LEMD3,
MLLT10,NPAT,NPHP3,NUP160,POLD3,PRPF4B,RLF,
SRSF10,SP1,SP3,U2SURP,STAG2,TERF1,ZNF280D

AGR2,AK7,BRIP1,CDC7,CHAF1B,CHRNA5,CLSPN,
DONSON,DTL,EXO1,FANCD2,FEN1,GMDS,KCNE3,
MCM6,POLD3,RNF138,STT3A,USP1,WDR76,XBP1
DDX21,EXOSC9,GNL2,GTPBP4,LTV1,LYAR,MAK16,
NIFK,FAM224B,NOP16,NOP58,ODC1,PNPT1,POLD3,
PRPF4,RIOK1,SERPINB8,SRSF7,TFPI2,TRMT6,XIRP1
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 POLD3
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA134868595; -.
Organism-specific databasesCTD 10714; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01050polymerase (DNA-directed), delta 3, accessory subunitapprovedIbuprofen


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Cross referenced IDs for POLD3
* 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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