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 HK1
Basic gene info.Gene symbolHK1
Gene namehexokinase 1
SynonymsHK1-ta|HK1-tb|HK1-tc|HKD|HKI|HMSNR|HXK1
CytomapUCSC genome browser: 10q22
Genomic locationchr10 :71075609-71161637
Type of geneprotein-coding
RefGenesNM_000188.2,
NM_033496.2,NM_033497.2,NM_033498.2,NM_033500.2,
Ensembl idENSG00000156515
DescriptionHK Ibrain form hexokinaseglycolytic enzymehexokinase type Ihexokinase-1
Modification date20141207
dbXrefs MIM : 142600
HGNC : HGNC
Ensembl : ENSG00000156515
HPRD : 00809
Vega : OTTHUMG00000018380
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HK1
BioGPS: 3098
Gene Expression Atlas: ENSG00000156515
The Human Protein Atlas: ENSG00000156515
PathwayNCI Pathway Interaction Database: HK1
KEGG: HK1
REACTOME: HK1
ConsensusPathDB
Pathway Commons: HK1
MetabolismMetaCyc: HK1
HUMANCyc: HK1
RegulationEnsembl's Regulation: ENSG00000156515
miRBase: chr10 :71,075,609-71,161,637
TargetScan: NM_000188
cisRED: ENSG00000156515
ContextiHOP: HK1
cancer metabolism search in PubMed: HK1
UCL Cancer Institute: HK1
Assigned class in ccmGDBC

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Phenotypic Information for HK1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HK1
Familial Cancer Database: HK1
* 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
BIOCARTA_GLYCOLYSIS_PATHWAY
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: HK1
MedGen: HK1 (Human Medical Genetics with Condition)
ClinVar: HK1
PhenotypeMGI: HK1 (International Mouse Phenotyping Consortium)
PhenomicDB: HK1

Mutations for HK1
* 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
ovaryHK1chr107110994371109963HK1chr107110543371105453
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 HK1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW841510HK11108107116149871161605HK1103327107116131871161542
BE149450HK129161107113964571139779MTOR14940411116707411167330
AW903811HK17170107115193671154745HK1161313107116113471161286
BE162082HK134331107105059971050896HK1330484107105089871051052
BI055002HK1197107116139571161491EPN293341171922573619225983
W28999HK148304107114243971144237HK1299584107114458471149049
BI003573CYB56114171176151016161510318HK1157477107115854671161028
BC048213HK16341535107116076971161765GNL115342914618460181854676

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)                 
LOSS (# sample) 1           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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=65)
Stat. for Synonymous SNVs
(# total SNVs=28)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr10:71128288-71128288p.?3
chr10:71158533-71158533p.R857H3
chr10:71119674-71119674p.L87P3
chr10:71103597-71103597p.L30L2
chr10:71158494-71158494p.A844E2
chr10:71119661-71119661p.D83N2
chr10:71144659-71144659p.T613T2
chr10:71142350-71142350p.A462V2
chr10:71158402-71158402p.L813L2
chr10:71158414-71158414p.C817C2

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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
# sample51 14  3 3 11551  812 11
# mutation51 13  3 4 11851  814 16
nonsynonymous SNV3  9  3 3 1841  311 10
synonymous SNV21 4    1  101   53 6
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
chr10:71119674p.L83P,HK13
chr10:71119661p.D79N,HK12
chr10:71142486p.T503T,HK12
chr10:71142523p.V516I,HK12
chr10:71158533p.R853H,HK12
chr10:71124653p.R398C,HK11
chr10:71144154p.R539H,HK11
chr10:71075755p.M663I,HK11
chr10:71136809p.R910Q,HK11
chr10:71144669p.S32S,HK11

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 HK1 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 HK1

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

ALDH1A2,C10orf35,FAM227B,CDAN1,COPS2,CYP2C9,EIF4EBP2,
GALK2,HAUS2,HK1,LRRC57,NEUROG3,PCBD1,PIGB,
PRTG,SAR1A,SPANXD,SUPV3L1,TCTN3,TSPAN15,VPS26A
ABCF2,ABCF3,APEH,ATPAF2,ATPIF1,DCAF11,GPRC5C,
HK1,KCNJ11,KLC2,MARK4,PKM,PLIN3,PPP2R4,
PPP5C,PSMD3,PTGES2,REPIN1,STIP1,UBA1,USP5

ABLIM1,AKAP13,ANKFY1,C10orf54,EPHA4,FAM114A1,FLII,
GBF1,GLG1,HK1,MAP3K6,MYO1C,NFKB2,PTGFRN,
PTPN13,RAB27A,SGMS2,SMG6,STK10,SUFU,TNKS1BP1
AARS,ACTB,AGPAT4,LINC00346,CDC27,EHBP1L1,GALNT2,
HK1,KPNB1,MSN,PHTF1,PPP2R4,RAB3GAP1,RHBDD1,
RNGTT,SRP68,STAT5A,TMEM110,TUBB,VCP,WDR82
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 HK1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB02007hexokinase 1experimentalAlpha-D-Glucose-6-Phosphate
DB02379hexokinase 1experimentalBeta-D-Glucose
DB03431hexokinase 1experimentalAdenosine-5'-Diphosphate
DB04395hexokinase 1experimentalPhosphoaminophosphonic Acid-Adenylate Ester


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Cross referenced IDs for HK1
* 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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