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 GCK
Basic gene info.Gene symbolGCK
Gene nameglucokinase (hexokinase 4)
SynonymsFGQTL3|GK|GLK|HHF3|HK4|HKIV|HXKP|LGLK|MODY2
CytomapUCSC genome browser: 7p15.3-p15.1
Genomic locationchr7 :44183869-44229022
Type of geneprotein-coding
RefGenesNM_000162.3,
NM_033507.1,NM_033508.1,
Ensembl idENSG00000106633
DescriptionATP:D-hexose 6-phosphotransferaseHK IVglucokinasehexokinase D, pancreatic isozymehexokinase type IVhexokinase-4hexokinase-D
Modification date20141222
dbXrefs MIM : 138079
HGNC : HGNC
Ensembl : ENSG00000106633
HPRD : 00680
Vega : OTTHUMG00000022903
ProteinUniProt: P35557
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GCK
BioGPS: 2645
Gene Expression Atlas: ENSG00000106633
The Human Protein Atlas: ENSG00000106633
PathwayNCI Pathway Interaction Database: GCK
KEGG: GCK
REACTOME: GCK
ConsensusPathDB
Pathway Commons: GCK
MetabolismMetaCyc: GCK
HUMANCyc: GCK
RegulationEnsembl's Regulation: ENSG00000106633
miRBase: chr7 :44,183,869-44,229,022
TargetScan: NM_000162
cisRED: ENSG00000106633
ContextiHOP: GCK
cancer metabolism search in PubMed: GCK
UCL Cancer Institute: GCK
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for GCK(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GCK
Familial Cancer Database: GCK
* 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
KEGG_GALACTOSE_METABOLISM
KEGG_STARCH_AND_SUCROSE_METABOLISM
KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM 125851; phenotype.
138079; gene.
602485; phenotype.
606391; phenotype.
Orphanet 552; MODY syndrome.
79299; Hyperinsulinism due to glucokinase deficiency.
99885; Permanent neonatal diabetes mellitus.
DiseaseKEGG Disease: GCK
MedGen: GCK (Human Medical Genetics with Condition)
ClinVar: GCK
PhenotypeMGI: GCK (International Mouse Phenotyping Consortium)
PhenomicDB: GCK

Mutations for GCK
* 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
There's no inter-chromosomal structural variation.
- 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
ovaryGCKchr74420058444200604GCKchr74419979144199811
pancreasGCKchr74421027644210296chr74106726741067287
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 GCK related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF885201GCK14316274418419944184218FRA10AC1158209109545059795450648

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 # sample        1        
GAIN (# sample)        1        
LOSS (# sample)                 
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=31)
Stat. for Synonymous SNVs
(# total SNVs=31)
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
chr7:44190669-44190669p.F124F4
chr7:44189604-44189604p.V182V3
chr7:44193018-44193018p.L31L3
chr7:44190569-44190569p.E158K3
chr7:44189392-44189392p.E217K2
chr7:44187302-44187302p.L271L2
chr7:44186118-44186118p.S322S2
chr7:44190560-44190560p.D161N2
chr7:44198715-44198715p.A2V2
chr7:44189575-44189575p.R192Q2

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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
# sample33 142 5 1  1081  197 5
# mutation33 142 5 1  1091  248 7
nonsynonymous SNV 2 51 2    471  174 3
synonymous SNV31 91 3 1  62   74 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
chr7:44193018p.L30L,GCK3
chr7:44190669p.F123F,GCK3
chr7:44186118p.D113D,GCK2
chr7:44191894p.V181V,GCK2
chr7:44189392p.A2V2
chr7:44189604p.S321S,GCK2
chr7:44198715p.E216K,GCK2
chr7:44190560p.R43C,GCK1
chr7:44228525p.S433C,GCK1
chr7:44186117p.D278D,GCK1

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 GCK 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 GCK

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

APCS,APOA1,APOA2,APOA4,APOB,APOC3,C3P1,
C8A,C9,CREB3L3,CRP,F2,FABP1,FGF23,
GCKR,HP,ITIH3,MT1B,PLG,SERPINA7,SULT2A1
BMP1,C14orf177,C6,C7,CETP,CTSL,FLVCR2,
GCKR,GPR64,HMOX1,HTRA3,INSL4,KIR3DP1,MAPK11,
OR2AG1,OR8D1,RHOXF2B,SCARNA20,SNORA19,SPATA8,TMEM114

ADIPOR2,ANKRD2,C12orf5,CACNA1C,CHRNA6,DCP1B,FBXL14,
FKBP4,FOXM1,GCKR,GPR139,MEGF11,NKX6-3,OR9K2,
PARP11,PPY,TEAD4,TMEM132B,TMEM173,TTTY6B,TULP3
AFP,APC,CA3,DNAJB3,FAM66E,GCKR,GOLGA6L1,
IQUB,CEP104,LOC100128573,LINC01312,MGC45800,NHLH1,OGDH,
RIPPLY1,SENP2,SGMS2,SNRK,ST7-OT4,TMEM86B,UGT1A1
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 GCK
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P35557; -.
ChemistryChEMBL CHEMBL3820; -.
Organism-specific databasesPharmGKB PA28610; -.
Organism-specific databasesCTD 2645; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB02379glucokinase (hexokinase 4)experimentalBeta-D-Glucose
DB07358glucokinase (hexokinase 4)experimental2-amino-N-(4-methyl-1,3-thiazol-2-yl)-5-[(4-methyl-4H-1,2,4-triazol-3-yl)sulfanyl]benzamide
DB07359glucokinase (hexokinase 4)experimental3-[(4-fluorophenyl)sulfanyl]-N-(4-methyl-1,3-thiazol-2-yl)-6-[(4-methyl-4H-1,2,4-triazol-3-yl)sulfanyl]pyridine-2-carboxamide
DB08118glucokinase (hexokinase 4)experimental2-(methylamino)-N-(4-methyl-1,3-thiazol-2-yl)-5-[(4-methyl-4H-1,2,4-triazol-3-yl)sulfanyl]benzamide
DB08210glucokinase (hexokinase 4)experimental2-AMINO-4-FLUORO-5-[(1-METHYL-1H-IMIDAZOL-2-YL)SULFANYL]-N-(1,3-THIAZOL-2-YL)BENZAMIDE


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Cross referenced IDs for GCK
* 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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