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 PHKA2
Basic gene info.Gene symbolPHKA2
Gene namephosphorylase kinase, alpha 2 (liver)
SynonymsGSD9A|PHK|PYK|PYKL|XLG|XLG2
CytomapUCSC genome browser: Xp22.2-p22.1
Genomic locationchrX :18910415-19002480
Type of geneprotein-coding
RefGenesNM_000292.2,
Ensembl idENSG00000044446
Descriptionphosphorylase b kinase regulatory subunit alpha liver isoformphosphorylase b kinase regulatory subunit alpha, liver isoformphosphorylase kinase alpha L subunitphosphorylase kinase alpha-subunit
Modification date20141219
dbXrefs MIM : 300798
HGNC : HGNC
Ensembl : ENSG00000044446
HPRD : 02380
Vega : OTTHUMG00000021222
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PHKA2
BioGPS: 5256
Gene Expression Atlas: ENSG00000044446
The Human Protein Atlas: ENSG00000044446
PathwayNCI Pathway Interaction Database: PHKA2
KEGG: PHKA2
REACTOME: PHKA2
ConsensusPathDB
Pathway Commons: PHKA2
MetabolismMetaCyc: PHKA2
HUMANCyc: PHKA2
RegulationEnsembl's Regulation: ENSG00000044446
miRBase: chrX :18,910,415-19,002,480
TargetScan: NM_000292
cisRED: ENSG00000044446
ContextiHOP: PHKA2
cancer metabolism search in PubMed: PHKA2
UCL Cancer Institute: PHKA2
Assigned class in ccmGDBC

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Phenotypic Information for PHKA2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PHKA2
Familial Cancer Database: PHKA2
* 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
Orphanet
DiseaseKEGG Disease: PHKA2
MedGen: PHKA2 (Human Medical Genetics with Condition)
ClinVar: PHKA2
PhenotypeMGI: PHKA2 (International Mouse Phenotyping Consortium)
PhenomicDB: PHKA2

Mutations for PHKA2
* 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 PHKA2 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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=108)
Stat. for Synonymous SNVs
(# total SNVs=24)
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
chr23:18924631-18924631p.R930W3
chr23:18913260-18913260p.R1111Q2
chr23:18926166-18926166p.S790I2
chr23:18912416-18912416p.T1148M2
chr23:18918808-18918808p.R1013W2
chr23:18923936-18923936p.D950N2
chr23:18911622-18911622p.S1230L2
chr23:18913297-18913297p.S1099A2
chr23:18959735-18959735p.L259R2
chr23:18938281-18938281p.S611L2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample16224  7 2  155   117111
# mutation16223  7 2  165   118117
nonsynonymous SNV 3116  5 2  125   65113
synonymous SNV1318  2    4    53 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
chrX:18911701p.A1204T3
chrX:18923936p.T891M2
chrX:18943834p.V1124V2
chrX:18912487p.V235V2
chrX:18966934p.S1230L2
chrX:18924631p.D950N2
chrX:18911622p.T507T2
chrX:18961840p.I155I2
chrX:18924858p.R930W2
chrX:18942542p.L913L1

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 PHKA2 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 PHKA2

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

CTPS2,CXorf23,FAM156A,GEMIN8,HDAC6,KLHL15,LPIN3,
MBTPS2,OGT,PDHA1,PHKA2,PMS2P3,PNPLA7,POLA1,
TCEANC,TRAPPC2,TTLL3,TXLNG,ZNF182,ZNF491,ZRSR2
ABCD2,ADCY6,ADIPOQ,ANO6,GPATCH11,EHHADH,GABRE,
GYG2,HK2,LPL,MESTIT1,MARC1,PCYOX1,PDE3B,
PDP2,PEX19,PHKA2,PRKAR2B,PTPLB,SIK2,SLC16A7

CASK,CCDC22,CLCN5,AMER1,GRIPAP1,HDAC6,LAS1L,
NONO,OTUD5,JADE3,PHF8,PHKA2,POLA1,SCML1,
TAB3,TSR2,USP27X,ZNF182,ZNF275,KRBOX4,ZNF674
ACAD10,C11orf49,DTX4,ERBB2,FAM53B,FOXO4,INSR,
KIAA0195,LRP4,MAML3,MYO1D,NDRG1,PAQR5,PFKL,
PHKA2,POMT1,PRKCSH,PTPRF,SCARB1,SORL1,ZNF395
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 PHKA2


There's no related Drug.
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Cross referenced IDs for PHKA2
* 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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