Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 HK1

Basic gene info.	Gene symbol	HK1
	Gene name	hexokinase 1
	Synonyms	HK1-ta\|HK1-tb\|HK1-tc\|HKD\|HKI\|HMSNR\|HXK1
	Cytomap	UCSC genome browser: 10q22
	Genomic location	chr10 :71075609-71161637
	Type of gene	protein-coding
	RefGenes	NM_000188.2, NM_033496.2,NM_033497.2,NM_033498.2,NM_033500.2,
	Ensembl id	ENSG00000156515
	Description	HK Ibrain form hexokinaseglycolytic enzymehexokinase type Ihexokinase-1
	Modification date	20141207
dbXrefs	MIM : 142600
	HGNC : HGNC
	Ensembl : ENSG00000156515
	HPRD : 00809
	Vega : OTTHUMG00000018380
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_HK1
	BioGPS: 3098
	Gene Expression Atlas: ENSG00000156515
	The Human Protein Atlas: ENSG00000156515
Pathway	NCI Pathway Interaction Database: HK1
	KEGG: HK1
	REACTOME: HK1
	ConsensusPathDB
	Pathway Commons: HK1
Metabolism	MetaCyc: HK1
	HUMANCyc: HK1
Regulation	Ensembl's Regulation: ENSG00000156515
	miRBase: chr10 :71,075,609-71,161,637
	TargetScan: NM_000188
	cisRED: ENSG00000156515
Context	iHOP: HK1
	cancer metabolism search in PubMed: HK1
	UCL Cancer Institute: HK1
Assigned class in ccmGDB	C

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Phenotypic Information for HK1(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic 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

Others
OMIM
Orphanet
Disease	KEGG Disease: HK1
	MedGen: HK1 (Human Medical Genetics with Condition)
	ClinVar: HK1
Phenotype	MGI: HK1 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	HK1	chr10	71109943	71109963	HK1	chr10	71105433	71105453

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows HK1 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
AW841510	HK1	1	108	10	71161498	71161605	HK1	103	327	10	71161318	71161542
BE149450	HK1	29	161	10	71139645	71139779	MTOR	149	404	1	11167074	11167330
AW903811	HK1	7	170	10	71151936	71154745	HK1	161	313	10	71161134	71161286
BE162082	HK1	34	331	10	71050599	71050896	HK1	330	484	10	71050898	71051052
BI055002	HK1	1	97	10	71161395	71161491	EPN2	93	341	17	19225736	19225983
W28999	HK1	48	304	10	71142439	71144237	HK1	299	584	10	71144584	71149049
BI003573	CYB561	14	171	17	61510161	61510318	HK1	157	477	10	71158546	71161028
BC048213	HK1	634	1535	10	71160769	71161765	GNL1	1534	2914	6	1846018	1854676

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr10:71128288-71128288	p.?	3
chr10:71158533-71158533	p.R857H	3
chr10:71119674-71119674	p.L87P	3
chr10:71103597-71103597	p.L30L	2
chr10:71158494-71158494	p.A844E	2
chr10:71119661-71119661	p.D83N	2
chr10:71144659-71144659	p.T613T	2
chr10:71142350-71142350	p.A462V	2
chr10:71158402-71158402	p.L813L	2
chr10:71144154-71144154	p.R550C	2

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	5	1		14			3		3		1	15	5	1			8	12		11
# mutation	5	1		13			3		4		1	18	5	1			8	14		16
nonsynonymous SNV	3			9			3		3		1	8	4	1			3	11		10
synonymous SNV	2	1		4					1			10	1				5	3		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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr10:71119674	p.L83P,HK1	3
chr10:71119661	p.T503T,HK1	2
chr10:71142486	p.V516I,HK1	2
chr10:71142523	p.R853H,HK1	2
chr10:71158533	p.D79N,HK1	2
chr10:71129353	p.N287N,HK1	1
chr10:71144653	p.L499L,HK1	1
chr10:71048521	p.T609T,HK1	1
chr10:71142254	p.V826L,HK1	1
chr10:71152041	p.K15K,HK1	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB02007	hexokinase 1	experimental	Alpha-D-Glucose-6-Phosphate
DB02379	hexokinase 1	experimental	Beta-D-Glucose
DB03431	hexokinase 1	experimental	Adenosine-5'-Diphosphate
DB04395	hexokinase 1	experimental	Phosphoaminophosphonic 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