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 POLD2
Basic gene info.Gene symbolPOLD2
Gene namepolymerase (DNA directed), delta 2, accessory subunit
Synonyms-
CytomapUCSC genome browser: 7p13
Genomic locationchr7 :44154278-44163169
Type of geneprotein-coding
RefGenesNM_001127218.2,
NM_001256879.1,NM_006230.3,
Ensembl idENSG00000106628
DescriptionDNA polymerase delta subunit 2DNA polymerase delta subunit p50Pol delta B subunit (p50)polymerase (DNA directed), delta 2, regulatory subunit 50kDa
Modification date20141207
dbXrefs MIM : 600815
HGNC : HGNC
Ensembl : ENSG00000106628
HPRD : 15982
Vega : OTTHUMG00000022909
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_POLD2
BioGPS: 5425
Gene Expression Atlas: ENSG00000106628
The Human Protein Atlas: ENSG00000106628
PathwayNCI Pathway Interaction Database: POLD2
KEGG: POLD2
REACTOME: POLD2
ConsensusPathDB
Pathway Commons: POLD2
MetabolismMetaCyc: POLD2
HUMANCyc: POLD2
RegulationEnsembl's Regulation: ENSG00000106628
miRBase: chr7 :44,154,278-44,163,169
TargetScan: NM_001127218
cisRED: ENSG00000106628
ContextiHOP: POLD2
cancer metabolism search in PubMed: POLD2
UCL Cancer Institute: POLD2
Assigned class in ccmGDBC

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Phenotypic Information for POLD2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: POLD2
Familial Cancer Database: POLD2
* 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: POLD2
MedGen: POLD2 (Human Medical Genetics with Condition)
ClinVar: POLD2
PhenotypeMGI: POLD2 (International Mouse Phenotyping Consortium)
PhenomicDB: POLD2

Mutations for POLD2
* 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 POLD2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ447574POLD21813874415428644154406CHST14134568154076388440764316

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 1      1        
GAIN (# sample) 1      1        
LOSS (# sample)                 
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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=22)
Stat. for Synonymous SNVs
(# total SNVs=11)
Stat. for Deletions
(# total SNVs=1)
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
chr7:44156512-44156512p.D228D2
chr7:44156578-44156578p.G206G2
chr7:44157611-44157611p.C91W2
chr7:44156474-44156474p.V241G1
chr7:44157329-44157329p.P119S1
chr7:44155788-44155788p.M315I1
chr7:44161455-44161455p.E66D1
chr7:44156480-44156480p.S239F1
chr7:44157330-44157330p.L118L1
chr7:44155818-44155818p.T305T1

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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
# sample33 2  1 1  513  32 6
# mutation33 2  1 1  513  32 7
nonsynonymous SNV31 1  1 1  213  21 5
synonymous SNV 2 1       3    11 2
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
chr7:44156578p.G206G,POLD22
chr7:44156512p.D460N,POLD21
chr7:44157622p.S239F,POLD21
chr7:44155788p.L424M,POLD21
chr7:44156543p.D228D,POLD21
chr7:44161448p.N406S,POLD21
chr7:44155818p.L218R,POLD21
chr7:44156568p.P399Q,POLD21
chr7:44161501p.E210K,POLD21
chr7:44155847p.S345T,POLD21

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 POLD2 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 POLD2

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

BUD31,UQCC3,C14orf80,SNHG15,C7orf50,CCM2,CLPP,
DDX56,EIF3B,MRPL4,MRPS24,NDUFA11,NDUFS6,NSUN5,
NUDT1,POLD2,PPIA,PSMG3,NELFE,TBRG4,YKT6
ALKBH7,DNPH1,CLPP,COX4I1,EIF3I,EXOSC5,GRHPR,
IDH3G,MLST8,MRPL43,MRPL4,MRPS18A,MRPS2,NDUFA11,
PHB2,PHB,POLD2,RPS16,TIMM13,TUFM,TXN2

AIMP2,BZW2,MALSU1,DDX56,EIF3B,FTSJ2,GGCT,
HEATR2,LSM5,MRPS17,MRPS24,NUDT1,POLD2,PPIA,
PSMG3,RANBP1,RPA3,SLC25A39,TBRG4,TIMM13,ZMYND19
ASF1B,C16orf59,CDC45,CDC7,CHAF1B,FEN1,HAUS7,
KIAA1524,MCM7,MTHFD1,PKMYT1,POLD2,RAD54L,RANBP1,
RNASEH2A,RUVBL1,SNRPA,SSRP1,TCF19,TK1,TRAP1
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 POLD2
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
DB01050polymerase (DNA directed), delta 2, accessory subunitapprovedIbuprofen


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Cross referenced IDs for POLD2
* 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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