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 PHKA1
Basic gene info.Gene symbolPHKA1
Gene namephosphorylase kinase, alpha 1 (muscle)
SynonymsPHKA
CytomapUCSC genome browser: Xq12-q13
Genomic locationchrX :71798663-71934029
Type of geneprotein-coding
RefGenesNM_001122670.1,
NM_001172436.1,NM_002637.3,
Ensembl idENSG00000268579
Descriptionphosphorylase b kinase regulatory subunit alpha skeletal muscle isoformphosphorylase b kinase regulatory subunit alpha, skeletal muscle isoformphosphorylase kinase alpha M subunitphosphorylase kinase, alpha 1 (muscle), muscle glycogenosis
Modification date20141219
dbXrefs MIM : 311870
HGNC : HGNC
Ensembl : ENSG00000067177
HPRD : 02415
Vega : OTTHUMG00000022696
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PHKA1
BioGPS: 5255
Gene Expression Atlas: ENSG00000268579
The Human Protein Atlas: ENSG00000268579
PathwayNCI Pathway Interaction Database: PHKA1
KEGG: PHKA1
REACTOME: PHKA1
ConsensusPathDB
Pathway Commons: PHKA1
MetabolismMetaCyc: PHKA1
HUMANCyc: PHKA1
RegulationEnsembl's Regulation: ENSG00000268579
miRBase: chrX :71,798,663-71,934,029
TargetScan: NM_001122670
cisRED: ENSG00000268579
ContextiHOP: PHKA1
cancer metabolism search in PubMed: PHKA1
UCL Cancer Institute: PHKA1
Assigned class in ccmGDBC

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Phenotypic Information for PHKA1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PHKA1
Familial Cancer Database: PHKA1
* 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: PHKA1
MedGen: PHKA1 (Human Medical Genetics with Condition)
ClinVar: PHKA1
PhenotypeMGI: PHKA1 (International Mouse Phenotyping Consortium)
PhenomicDB: PHKA1

Mutations for PHKA1
* 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 PHKA1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA328772PHKA1885X7188046871880545OLFML2B801881161953016161953124
AI174654PHKA1183X7180017371800553PHKA180262X7180050871800690

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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=100)
Stat. for Synonymous SNVs
(# total SNVs=20)
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
chr23:71870282-71870282p.R428C3
chr23:71932665-71932665p.A65S2
chr23:71840661-71840661p.G684E2
chr23:71830999-71830999p.R802L2
chr23:71802268-71802268p.D1160Y2
chr23:71821870-71821870p.R1015C2
chr23:71822975-71822975p.R971*2
chr23:71825180-71825180p.R919Q2
chr23:71823017-71823017p.L957F2
chr23:71925089-71925089p.V81V2

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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
# sample44193 2 42 95511197115
# mutation441103 2 42 95511207123
nonsynonymous SNV43182 1 32 75511165 19
synonymous SNV 1 21 1 1  2    4214
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:71840645p.R428C,PHKA12
chrX:71932665p.A65T,PHKA12
chrX:71870282p.F689L,PHKA12
chrX:71802268p.D1088N,PHKA12
chrX:71856223p.R491R,PHKA12
chrX:71830999p.R743L,PHKA12
chrX:71840634p.R1015H1
chrX:71876083p.R743W,PHKA11
chrX:71813013p.E624K,PHKA11
chrX:71823002p.I471I,PHKA11

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 PHKA1 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 PHKA1

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

APOOL,ATRX,CLCN3,FAM120C,FAM122B,FAM199X,FBXO21,
LARP4,MBTPS2,MED14,OCRL,PEX1,PHKA1,RBM41,
RLIM,RPS6KA6,TAF1,TMEM209,YIPF6,ZFX,ZXDB
ASB14,ASB4,CA14,CEP85,CMYA5,STRIP2,FEM1A,
JPH1,KCNQ5,MYBPC1,MYLK4,OBSCN,PFKM,PHKA1,
PKIA,PPP2R3A,PRKAA2,SLC25A12,TXLNB,UGT3A1,WDR62

AMMECR1,APEX2,ATP11C,ERCC6L,FAM199X,IRAK1,LAS1L,
MTMR1,NKRF,NONO,OCRL,PHKA1,PRPS1,RLIM,
SLC10A3,SLC25A43,SMS,UBQLN2,UPRT,ZBTB33,ZNF275
ARMCX3,ARSB,ARSJ,C11orf84,C17orf51,WDPCP,CCDC149,
COPS7B,CYB5D1,DAAM1,DHX57,IFT81,INTU,MAGEF1,
FAN1,PHKA1,SHANK2,TCOF1,TSR1,TULP3,ZNF154
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 PHKA1


There's no related Drug.
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Cross referenced IDs for PHKA1
* 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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