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 HK2
Basic gene info.Gene symbolHK2
Gene namehexokinase 2
SynonymsHKII|HXK2
CytomapUCSC genome browser: 2p13
Genomic locationchr2 :75059781-75120481
Type of geneprotein-coding
RefGenesNM_000189.4,
Ensembl idENSG00000159399
DescriptionHK IIhexokinase type IIhexokinase-2hexokinase-2, musclemuscle form hexokinase
Modification date20141207
dbXrefs MIM : 601125
HGNC : HGNC
Ensembl : ENSG00000159399
HPRD : 03080
Vega : OTTHUMG00000129972
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HK2
BioGPS: 3099
Gene Expression Atlas: ENSG00000159399
The Human Protein Atlas: ENSG00000159399
PathwayNCI Pathway Interaction Database: HK2
KEGG: HK2
REACTOME: HK2
ConsensusPathDB
Pathway Commons: HK2
MetabolismMetaCyc: HK2
HUMANCyc: HK2
RegulationEnsembl's Regulation: ENSG00000159399
miRBase: chr2 :75,059,781-75,120,481
TargetScan: NM_000189
cisRED: ENSG00000159399
ContextiHOP: HK2
cancer metabolism search in PubMed: HK2
UCL Cancer Institute: HK2
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of HK2 in cancer cell metabolism1. Kim H, Jang H, Kim TW, Kang BH, Lee SE, et al. (2015) Core Pluripotency Factors Directly Regulate Metabolism in Embryonic Stem Cell to Maintain Pluripotency. Stem Cells. doi: 10.1002/stem.2073. go to article
2. Zhuo B, Li Y, Li Z, Qin H, Sun Q, et al. (2015) PI3K/Akt signaling mediated Hexokinase-2 expression inhibits cell apoptosis and promotes tumor growth in pediatric osteosarcoma. Biochem Biophys Res Commun. doi: 10.1016/j.bbrc.2015.06.092 go to article
3. Guo W, Qiu Z, Wang Z, Wang Q, Tan N, et al. (2015) MiR-199a-5p is negatively associated with malignancies and regulates glycolysis and lactate production by targeting hexokinase 2 in liver cancer. Hepatology. doi: 10.1002/hep.27929. go to article
4. Alvarez JV, Belka GK, Pan TC, Chen CC, Blankemeyer E, et al. (2014) Oncogene pathway activation in mammary tumors dictates FDG-PET uptake. Cancer Res 74: 7583-7598. doi: 10.1158/0008-5472.CAN-14-1235. pmid: 4342047. go to article

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Phenotypic Information for HK2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HK2
Familial Cancer Database: HK2
* 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_FRUCTOSE_AND_MANNOSE_METABOLISM
KEGG_GALACTOSE_METABOLISM
KEGG_STARCH_AND_SUCROSE_METABOLISM
KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: HK2
MedGen: HK2 (Human Medical Genetics with Condition)
ClinVar: HK2
PhenotypeMGI: HK2 (International Mouse Phenotyping Consortium)
PhenomicDB: HK2

Mutations for HK2
* 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 HK2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
Z46376FAM50A11069X153674037153678996HK21067528927506128475119113

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  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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=68)
Stat. for Synonymous SNVs
(# total SNVs=27)
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
chr2:75081444-75081444p.R30C3
chr2:75115108-75115108p.L766L3
chr2:75061718-75061718p.S4L3
chr2:75113668-75113668p.V696E2
chr2:75115074-75115074p.R755H2
chr2:75107455-75107455p.L443L2
chr2:75081481-75081481p.R42Q2
chr2:75113426-75113426p.F647L2
chr2:75109306-75109306p.G593G2
chr2:75061723-75061723p.L6L2

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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
# sample22 82 4 2  1162  1410214
# mutation22 92 4 2  1362  1513214
nonsynonymous SNV22 62 4    1162  101029
synonymous SNV   3    2  2    53 5
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
chr2:75061718p.S4W3
chr2:75117984p.R702Q2
chr2:75113788p.P736H2
chr2:75113686p.F890F2
chr2:75099464p.I781I1
chr2:75112644p.A902T1
chr2:75104355p.V186A1
chr2:75113751p.R444C1
chr2:75061762p.G660R1
chr2:75107651p.E783Q1

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 HK2 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 HK2

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

AFF3,AHCYL2,ATP2C2,BCAS1,BZW1,CADPS,CLCN3,
EPT1,GDPD1,GMCL1,GUF1,HK2,ISOC1,MAP4K3,
KAT6B,RAB3A,RELL1,SYNJ2BP,TRIM36,ZFHX3,ZSWIM5
ACO1,AOC3,DMGDH,ESYT1,FZD4,GPAM,GPD1,
HK2,LPL,MRAS,MTHFD1,NAT8L,PEX19,PLIN1,
PRKAR2B,PXDN,PYGL,RBP4,TNS1,TSPAN3,VKORC1L1

BMP2,C4orf19,CASP5,CCL28,CEACAM1,CEACAM7,DUOX2,
DUOXA2,GOLM1,HK2,ITM2C,LIMA1,MALL,NR3C2,
PAPSS2,PIGR,PTPRH,RBM47,TMPRSS2,TRIM40,XDH
BAIAP2L1,CASP10,CEACAM1,CEACAM5,CEACAM6,CHD1,CLIC5,
DNAJC3,DNAJC7,DTX3L,HK2,HPSE,LEO1,MUC1,
RNF19B,RPS6KA4,SLCO2A1,TOP1,TRIM15,USP38,XDH
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 HK2


There's no related Drug.
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Cross referenced IDs for HK2
* 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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