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 PGK2
Basic gene info.Gene symbolPGK2
Gene namephosphoglycerate kinase 2
SynonymsHEL-S-272|PGKB|PGKPS|dJ417L20.2
CytomapUCSC genome browser: 6p12.3
Genomic locationchr6 :49753363-49755053
Type of geneprotein-coding
RefGenesNM_138733.4,
Ensembl idENSG00000170950
Descriptionepididymis secretory protein Li 272phosphoglycerate kinase autosomal pseudogenephosphoglycerate kinase, testis specific
Modification date20141207
dbXrefs MIM : 172270
HGNC : HGNC
HPRD : 01393
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PGK2
BioGPS: 5232
Gene Expression Atlas: ENSG00000170950
The Human Protein Atlas: ENSG00000170950
PathwayNCI Pathway Interaction Database: PGK2
KEGG: PGK2
REACTOME: PGK2
ConsensusPathDB
Pathway Commons: PGK2
MetabolismMetaCyc: PGK2
HUMANCyc: PGK2
RegulationEnsembl's Regulation: ENSG00000170950
miRBase: chr6 :49,753,363-49,755,053
TargetScan: NM_138733
cisRED: ENSG00000170950
ContextiHOP: PGK2
cancer metabolism search in PubMed: PGK2
UCL Cancer Institute: PGK2
Assigned class in ccmGDBC

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Phenotypic Information for PGK2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PGK2
Familial Cancer Database: PGK2
* 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_GLYCOLYSIS_GLUCONEOGENESIS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PGK2
MedGen: PGK2 (Human Medical Genetics with Condition)
ClinVar: PGK2
PhenotypeMGI: PGK2 (International Mouse Phenotyping Consortium)
PhenomicDB: PGK2

Mutations for PGK2
* 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 PGK2 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=7

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=65)
Stat. for Synonymous SNVs
(# total SNVs=26)
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
chr6:49754595-49754595p.A102A4
chr6:49754498-49754498p.P135S3
chr6:49754005-49754005p.G299E3
chr6:49753713-49753713p.G396G3
chr6:49754266-49754266p.L212R3
chr6:49754598-49754598p.G101G3
chr6:49754337-49754337p.F188L3
chr6:49754076-49754076p.K275N3
chr6:49754580-49754580p.A107A2
chr6:49753680-49753680p.I407I2

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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
# sample12 122 2 1  2071  386 9
# mutation12 132 2 1  2371  386 9
nonsynonymous SNV   91 1    1741  223 5
synonymous SNV12 41 1 1  63   163 4
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
chr6:49754595p.A102A4
chr6:49754498p.G396G3
chr6:49753713p.P135S3
chr6:49754076p.L212R2
chr6:49754266p.D145E2
chr6:49754784p.A102S2
chr6:49754123p.G101G2
chr6:49754528p.G277D2
chr6:49754597p.K275N2
chr6:49754598p.R39R2

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 PGK2 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 PGK2

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

ABCC6P1,BSND,MIEN1,C2orf54,CRISP2,CRISP3,CRYBA4,
ERBB2,GRB7,IRGC,MDC1,PGK2,PPP1R1B,PSMD3,
RHAG,SP8,STARD3,STRA8,SULT1A2,SUN3,ZFP57
CD163L1,CFHR1,CXorf21,DNTT,FAM105A,FPR3,KIR2DS4,
KRTAP12-2,LUZP4,MARCH1,MPEG1,OPN1LW,OR56A5,OR5AK2,
OR7E5P,PGK2,PRG4,RGS18,PMEL,TCHH,TREML3P

APOC1P1,DHRS4L1,HIST1H4K,LOC286135,LOC653544,MORF4,PGK2,
POTEE,RBMY1A1,RPL13AP20,RPS10P7,RPS26P11,RPSAP9,SNORA24,
TPI1P3,Z
ABCC12,ANO4,CALML5,CCDC63,DPCR1,FGF22,GUCY2EP,
LOC100133920,MUCL1,NKX6-1,OR4A16,OR6B2,OR7E24,OR8D2,
PGK2,PIP,IER3___SRGN,RBMY1A1,SNORA13,SNORA58,WFDC8
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 PGK2


There's no related Drug.
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Cross referenced IDs for PGK2
* 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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