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 POLD1
Basic gene info.Gene symbolPOLD1
Gene namepolymerase (DNA directed), delta 1, catalytic subunit
SynonymsCDC2|CRCS10|MDPL|POLD
CytomapUCSC genome browser: 19q13.3
Genomic locationchr19 :50887579-50921275
Type of geneprotein-coding
RefGenesNM_001256849.1,
NM_002691.3,NR_046402.1,
Ensembl idENSG00000062822
DescriptionCDC2 homologDNA polymerase delta catalytic subunitDNA polymerase subunit delta p125polymerase (DNA directed), delta 1, catalytic subunit 125kDa
Modification date20141207
dbXrefs MIM : 174761
HGNC : HGNC
Ensembl : ENSG00000062822
HPRD : 08882
Vega : OTTHUMG00000183037
ProteinUniProt: P28340
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_POLD1
BioGPS: 5424
Gene Expression Atlas: ENSG00000062822
The Human Protein Atlas: ENSG00000062822
PathwayNCI Pathway Interaction Database: POLD1
KEGG: POLD1
REACTOME: POLD1
ConsensusPathDB
Pathway Commons: POLD1
MetabolismMetaCyc: POLD1
HUMANCyc: POLD1
RegulationEnsembl's Regulation: ENSG00000062822
miRBase: chr19 :50,887,579-50,921,275
TargetScan: NM_001256849
cisRED: ENSG00000062822
ContextiHOP: POLD1
cancer metabolism search in PubMed: POLD1
UCL Cancer Institute: POLD1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of POLD1 in cancer cell metabolism1. Mertz TM, Sharma S, Chabes A, Shcherbakova PV (2015) Colon cancer-associated mutator DNA polymerase δ variant causes expansion of dNTP pools increasing its own infidelity. Proceedings of the National Academy of Sciences 112: E2467-E2476. go to article

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Phenotypic Information for POLD1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: POLD1
Familial Cancer Database: POLD1
* 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 174761; gene.
612591; phenotype.
615381; phenotype.
Orphanet 363649; Mandibular hypoplasia-deafness-progeroid syndrome.
DiseaseKEGG Disease: POLD1
MedGen: POLD1 (Human Medical Genetics with Condition)
ClinVar: POLD1
PhenotypeMGI: POLD1 (International Mouse Phenotyping Consortium)
PhenomicDB: POLD1

Mutations for POLD1
* 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 POLD1 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
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=70)
Stat. for Synonymous SNVs
(# total SNVs=26)
Stat. for Deletions
(# total SNVs=5)
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
chr19:50906815-50906815p.F401F3
chr19:50918720-50918720p.A864T3
chr19:50905959-50905959p.R311C2
chr19:50905595-50905595p.F241F2
chr19:50912864-50912864p.S699T2
chr19:50912086-50912086p.Y607C2
chr19:50918097-50918097p.S805N2
chr19:50916686-50916686p.V720I2
chr19:50905055-50905055p.P116fs*532
chr19:50909504-50909504p.F436L2

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample111181 4 3  432 11311 14
# mutation111171 4 3  532 11412 16
nonsynonymous SNV11 121 3 2  42  168 11
synonymous SNV  15  1 1  112  84 5
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
chr19:50905595p.V392M,POLD12
chr19:50906786p.F401F,POLD12
chr19:50905152p.A864T,POLD12
chr19:50906815p.F241F,POLD12
chr19:50918720p.Q461H,POLD12
chr19:50905959p.R311C,POLD12
chr19:50917112p.S788S,POLD12
chr19:50909579p.A145D,POLD12
chr19:50905974p.L852R,POLD11
chr19:50918097p.F1099L,POLD11

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 POLD1 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 POLD1

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

ATAD3A,BAX,BCL2L12,C19orf48,CCDC124,CDT1,CPSF4,
CTU1,DAZAP1,IRF3,LIG1,MCM5,MCM7,MXD3,
NUP62,PKMYT1,POLD1,PPAN,PRMT1,TCOF1,UBE2S
ARVCF,AXIN1,C17orf70,CC2D1A,CHERP,CHTF18,EHMT2,
FBXL19,GRK6,MCM5,POLD1,PUS1,RIN1,SLC12A9,
SNAPC4,SPPL2B,TCF3,TRAF2,TSC22D4,U2AF2,ZMYND19

BCL2L12,C16orf59,C17orf53,CDT1,CHAF1A,KIF18B,LIG1,
LMNB2,MCM2,PKMYT1,POLD1,POLE,PRPF31,RAD54L,
RUVBL2,TACC3,THOP1,TOMM40,TRIM28,UHRF1,WDR62
C14orf80,CDT1,CHAF1A,CHTF18,H2AFX,LIG1,LOC100128191,
LRRC45,MCM5,MED24,TONSL,POLD1,PPP2R3B,RECQL4,
REEP4,SPC24,SYMPK,TACC3,TARS2,U2AF2,ZNF296
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 POLD1


There's no related Drug.
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Cross referenced IDs for POLD1
* 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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