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 POLA2
Basic gene info.Gene symbolPOLA2
Gene namepolymerase (DNA directed), alpha 2, accessory subunit
Synonyms-
CytomapUCSC genome browser: 11q13.1
Genomic locationchr11 :65029431-65065088
Type of geneprotein-coding
RefGenesNM_002689.2,
Ensembl idENSG00000014138
DescriptionDNA polymerase alpha 70 kDa subunitDNA polymerase alpha subunit Bpolymerase (DNA directed), alpha 2 (70kD subunit)polymerase (DNA-directed), alpha (70kD)
Modification date20141207
dbXrefs HGNC : HGNC
HPRD : 10160
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_POLA2
BioGPS: 23649
Gene Expression Atlas: ENSG00000014138
The Human Protein Atlas: ENSG00000014138
PathwayNCI Pathway Interaction Database: POLA2
KEGG: POLA2
REACTOME: POLA2
ConsensusPathDB
Pathway Commons: POLA2
MetabolismMetaCyc: POLA2
HUMANCyc: POLA2
RegulationEnsembl's Regulation: ENSG00000014138
miRBase: chr11 :65,029,431-65,065,088
TargetScan: NM_002689
cisRED: ENSG00000014138
ContextiHOP: POLA2
cancer metabolism search in PubMed: POLA2
UCL Cancer Institute: POLA2
Assigned class in ccmGDBC

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Phenotypic Information for POLA2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: POLA2
Familial Cancer Database: POLA2
* 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: POLA2
MedGen: POLA2 (Human Medical Genetics with Condition)
ClinVar: POLA2
PhenotypeMGI: POLA2 (International Mouse Phenotyping Consortium)
PhenomicDB: POLA2

Mutations for POLA2
* 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 POLA2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI010845EIF3B21152724187722419055POLA2146303116504720265047359
BC015618RPL1044549X153628152153629254POLA25503007116502945165065088

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 # sample1                
GAIN (# sample)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=33)
Stat. for Synonymous SNVs
(# total SNVs=12)
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
chr11:65062070-65062070p.F469F2
chr11:65034053-65034053p.L27S2
chr11:65034164-65034164p.S64Y2
chr11:65048610-65048610p.P298T2
chr11:65064614-65064614p.V557V2
chr11:65056524-65056524p.G379S1
chr11:65043371-65043371p.Q121H1
chr11:65046311-65046311p.I191T1
chr11:65061716-65061716p.S446F1
chr11:65049163-65049163p.N308S1

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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
# sample21 81 1    73 1 53 3
# mutation21 81 1    94 1 53 3
nonsynonymous SNV2  61 1    61 1 33 2
synonymous SNV 1 2       33   2  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
chr11:65062070p.F469F2
chr11:65046289p.S418F1
chr11:65055233p.Q211Q1
chr11:65062097p.P433H1
chr11:65046311p.V251V1
chr11:65055237p.S443S1
chr11:65062101p.G255C1
chr11:65046372p.R276R1
chr11:65055264p.F478F1
chr11:65063424p.L296V1

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 POLA2 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 POLA2

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

ASF1B,CCNB2,CDC25A,CDC45,CDCA5,CDT1,CTPS1,
DPF2,FEN1,FOXM1,KIF2C,KIF4A,KIFC1,MCM2,
OIP5,ORC1,POLA2,RAD51,RAD54L,TROAP,TUBA1B
ARHGEF19,BAIAP2L1,DNAJC9,GINS2,GLB1L2,GYLTL1B,LIG1,
MCM2,MCM3,MCM5,MOV10,NFKBIE,NUP62,PLEK2,
POLA2,RPS6KA1,SAMD10,SEMA4A,TCF19,TP53,TRAIP

ASF1B,CDC20,CDC45,CDCA5,CENPM,CHAF1B,CHEK1,
FEN1,GINS3,HELLS,MCM2,MCM5,MCM6,ORC1,
POC1A,POLA2,RAD51,RAD54L,RCC1,XRCC3,ZWINT
ASF1B,C1orf112,CDC45,CDCA5,CHAF1B,DSCC1,EXO1,
FEN1,GINS4,MCM10,MCM6,MCM7,MELK,ORC1,
POLA2,RFC3,RFC5,RRM2,TCF19,TRIP13,ZWILCH
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 POLA2
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
DB00851polymerase (DNA directed), alpha 2, accessory subunitapprovedDacarbazine
DB00441polymerase (DNA directed), alpha 2, accessory subunitapprovedGemcitabine
DB01050polymerase (DNA directed), alpha 2, accessory subunitapprovedIbuprofen


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Cross referenced IDs for POLA2
* 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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