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 PRIM2
Basic gene info.Gene symbolPRIM2
Gene nameprimase, DNA, polypeptide 2 (58kDa)
SynonymsPRIM2A|p58
CytomapUCSC genome browser: 6p12-p11.1
Genomic locationchr6 :57182421-57513376
Type of geneprotein-coding
RefGenesNM_000947.4,
NM_001282487.1,NM_001282488.1,
Ensembl idENSG00000146143
DescriptionDNA primase 58 kDa subunitDNA primase large subunit
Modification date20141212
dbXrefs MIM : 176636
HGNC : HGNC
Ensembl : ENSG00000146143
HPRD : 08900
Vega : OTTHUMG00000016190
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PRIM2
BioGPS: 5558
Gene Expression Atlas: ENSG00000146143
The Human Protein Atlas: ENSG00000146143
PathwayNCI Pathway Interaction Database: PRIM2
KEGG: PRIM2
REACTOME: PRIM2
ConsensusPathDB
Pathway Commons: PRIM2
MetabolismMetaCyc: PRIM2
HUMANCyc: PRIM2
RegulationEnsembl's Regulation: ENSG00000146143
miRBase: chr6 :57,182,421-57,513,376
TargetScan: NM_000947
cisRED: ENSG00000146143
ContextiHOP: PRIM2
cancer metabolism search in PubMed: PRIM2
UCL Cancer Institute: PRIM2
Assigned class in ccmGDBC

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Phenotypic Information for PRIM2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PRIM2
Familial Cancer Database: PRIM2
* 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: PRIM2
MedGen: PRIM2 (Human Medical Genetics with Condition)
ClinVar: PRIM2
PhenotypeMGI: PRIM2 (International Mouse Phenotyping Consortium)
PhenomicDB: PRIM2

Mutations for PRIM2
* 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
ovaryPRIM2chr65735915257359172PRIM2chr65737121857371238
ovaryPRIM2chr65738615757386177PRIM2chr65738898157389001
ovaryPRIM2chr65738653057386550PRIM2chr65738665257386672
ovaryPRIM2chr65739258857392608chr65440803854408058
ovaryPRIM2chr65740046057400480PRIM2chr65740062057400640
pancreasPRIM2chr65727820757278227PRIM2chr65728099157281011
pancreasPRIM2chr65729717457297194PRIM2chr65730123257301252
pancreasPRIM2chr65730133157301351PRIM2chr65730148457301504
pancreasPRIM2chr65730870357308723chr960657246065744
pancreasPRIM2chr65738185557381875PRIM2chr65738208957382109
pancreasPRIM2chr65738918057389200PRIM2chr65739000657390026
pancreasPRIM2chr65741693557416955PRIM2chr65741856957418589
pancreasPRIM2chr65744365557443855PRIM2chr65742508257425282
pancreasPRIM2chr65744696257446982PRIM2chr65745000257450022
pancreasPRIM2chr65747297257472992PRIM2chr65749313157493151
pancreasPRIM2chr65747589957475919chr192322045523220475
pancreasPRIM2chr65748165157481671PRIM2chr65748170157481721
pancreasPRIM2chr65749811957498139PRIM2chr65749821857498238
prostatePRIM2chr65741745757417457PRIM2chr65743283457432834
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 PRIM2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
EB362401PRIM2194165734032957340351CRYAB2732311111779352111779648
BQ345327ACP6834931147119192147119602PRIM248756365734328857343364

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 # sample9  1    14 10  85 2
GAIN (# sample)8  1    9 10  85 2
LOSS (# sample)1       5        
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=89)		Stat. for Synonymous SNVs
(# total SNVs=20)
Stat. for Deletions
(# total SNVs=0)		Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr6:57512667-57512667p.E499*5
chr6:57393160-57393160p.K270K4
chr6:57512544-57512544p.G458R3
chr6:57398207-57398207p.G304*3
chr6:57512650-57512650p.S493Y3
chr6:57512666-57512666p.M498I3
chr6:57467125-57467125p.E356Q2
chr6:57472395-57472395p.K395R2
chr6:57512615-57512615p.K481N2
chr6:57467180-57467180p.N374S2

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1  1    2  1     2  
# mutation1  1    2  1     2  
nonsynonymous SNV   1    1  1     1  
synonymous SNV1       1        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
chr6:57185282p.R118C,PRIM21
chr6:57185310p.L11L,PRIM21
chr6:57190736p.R18M,PRIM21
chr6:57183276p.S21S,PRIM21
chr6:57183296p.E57D,PRIM21
chr6:57183306p.V61E,PRIM21
chr6:57185271p.Y70Y,PRIM21

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 PRIM2 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 PRIM2

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

BUB1,CEP55,DEK,EXO1,GMPS,KIF11,KIF18A,
KIF20A,KIF23,KIF4A,KIFC1,MCM3,MELK,MKI67,
NCAPH,PRIM2,SRPK1,STIL,SYNCRIP,TPX2,TTK		ACTL6A,SAYSD1,CD47,CNOT10,COIL,COMMD2,DDX20,
FAM60A,FBXO5,GABPB1,LRRC8D,POT1,PRIM2,RFC3,
SUDS3,TDP1,TMEM123,TTC19,WDR89,ZNF140,ZNF146

ACTL6A,CMSS1,CENPQ,CIRH1A,MTFR2,FBXO5,GLO1,
PAK1IP1,PEX3,PPIL1,PRIM1,PRIM2,RFC4,RNASEH2A,
SRSF3,SRSF7,SNRPC,SPC25,TCP1,TTK,USP39		C1orf112,CDC23,CHCHD3,CPSF3,CTCFL,EED,HNRNPL,
KARS,OIP5,ORC1,PCNA,POLA2,PRIM2,RAD18,
RAD21,RAD51,RAE1,RFC3,RFC5,XRCC5,XRCC6
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 PRIM2


There's no related Drug.
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Cross referenced IDs for PRIM2
* 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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