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 PHKG2
Basic gene info.Gene symbolPHKG2
Gene namephosphorylase kinase, gamma 2 (testis)
SynonymsGSD9C
CytomapUCSC genome browser: 16p11.2
Genomic locationchr16 :30759619-30772497
Type of geneprotein-coding
RefGenesNM_000294.2,
NM_001172432.1,
Ensembl idENSG00000156873
DescriptionPHK-gamma-LTPHK-gamma-TPSK-C3Phosphorylase kinase, gamma 2 (testis/liver)phosphorylase b kinase gamma catalytic chain, liver/testis isoformphosphorylase b kinase gamma catalytic chain, testis/liver isoformphosphorylase kinase subunit gamma-2serine/
Modification date20141222
dbXrefs MIM : 172471
HGNC : HGNC
Ensembl : ENSG00000156873
HPRD : 01405
Vega : OTTHUMG00000132400
ProteinUniProt: P15735
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PHKG2
BioGPS: 5261
Gene Expression Atlas: ENSG00000156873
The Human Protein Atlas: ENSG00000156873
PathwayNCI Pathway Interaction Database: PHKG2
KEGG: PHKG2
REACTOME: PHKG2
ConsensusPathDB
Pathway Commons: PHKG2
MetabolismMetaCyc: PHKG2
HUMANCyc: PHKG2
RegulationEnsembl's Regulation: ENSG00000156873
miRBase: chr16 :30,759,619-30,772,497
TargetScan: NM_000294
cisRED: ENSG00000156873
ContextiHOP: PHKG2
cancer metabolism search in PubMed: PHKG2
UCL Cancer Institute: PHKG2
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PHKG2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PHKG2
Familial Cancer Database: PHKG2
* 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
REACTOME_METABOLISM_OF_CARBOHYDRATES
REACTOME_GLUCOSE_METABOLISM

check002.gifOthers
OMIM 172471; gene.
613027; phenotype.
Orphanet 264580; Glycogen storage disease due to liver phosphorylase kinase deficiency.
DiseaseKEGG Disease: PHKG2
MedGen: PHKG2 (Human Medical Genetics with Condition)
ClinVar: PHKG2
PhenotypeMGI: PHKG2 (International Mouse Phenotyping Consortium)
PhenomicDB: PHKG2

Mutations for PHKG2
* 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
haematopoietic_and_lymphoid_tissuePHKG2chr163076328330763283PHKG2chr163076328330763283
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 PHKG2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF853022C16orf933305163077259830772901PHKG2299416163076884230768958

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

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=0)
Stat. for Synonymous SNVs
(# total SNVs=1)
There's no ns-snv.
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
chr16:30768418-30768418p.*407*1
chr16:30762590-30762590p.H87N1

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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
# sample2125  1    612  29 5
# mutation2125  1    712  29 5
nonsynonymous SNV2114  1    41   18 3
synonymous SNV  11       3 2  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
chr16:30764777p.R152Q,PHKG22
chr16:30767819p.Y193H,PHKG21
chr16:30768328p.R377R1
chr16:30762430p.G33G,PHKG21
chr16:30762916p.L194V,PHKG21
chr16:30767987p.G391G1
chr16:30768370p.R39L,PHKG21
chr16:30762447p.E197Q,PHKG21
chr16:30764566p.X407X1
chr16:30767997p.R44Q,PHKG21

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 PHKG2 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 PHKG2

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

CD2BP2,ECI1,FAM195A,FLYWCH2,GFER,SLX1B,INO80E,
JMJD8,MPG,KAT8,NME3,PHKG2,PIGQ,PPP4C,
PRR14,RHOT2,SPSB3,STX4,TMEM219,ZNF688,ZNF768
ATG4B,B3GAT3,BRMS1,VPS9D1,OXLD1,C19orf25,C9orf142,
COQ4,HMG20B,LYPLA2,NMRAL1,PHKG2,PIGQ,QTRT1,
RFXANK,SIRT6,TARBP2,TMEM141,TRAPPC6A,WDR34,ZNF446

AGAP4,ANKS3,ATG4B,BRICD5,C16orf93,CDK10,CENPT,
EGFL8,FAM73B,INO80E,KIAA0895L,KAT8,NPIPB3,PHKG2,
PRR14,RHOT2,SH2B1,TAF1C,TBC1D10B,ZNF768,ZNF789
ASPSCR1,AUP1,DFFB,DUS3L,FASTK,FLAD1,FPGS,
METTL17,MTX1,NOL12,PHKG2,PNKP,RASSF7,RPS6KB2,
RPUSD1,SLC25A10,TAZ,TRMU,UCKL1,YIF1B,ZSCAN5A
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 PHKG2


There's no related Drug.
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Cross referenced IDs for PHKG2
* 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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