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 GUK1

Basic gene info.	Gene symbol	GUK1
	Gene name	guanylate kinase 1
	Synonyms	GMK
	Cytomap	UCSC genome browser: 1q32-q41
	Genomic location	chr1 :228327928-228336655
	Type of gene	protein-coding
	RefGenes	NM_000858.5, NM_001159390.1,NM_001159391.1,NM_001242839.1,NM_001242840.1,
	Ensembl id	ENSG00000143774
	Description	ATP:GMP phosphotransferaseGMP kinaseguanylate kinase
	Modification date	20141207
dbXrefs	MIM : 139270
	HGNC : HGNC
	Ensembl : ENSG00000143774
	HPRD : 00755
	Vega : OTTHUMG00000039503
Protein	UniProt: Q16774 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GUK1
	BioGPS: 2987
	Gene Expression Atlas: ENSG00000143774
	The Human Protein Atlas: ENSG00000143774
Pathway	NCI Pathway Interaction Database: GUK1
	KEGG: GUK1
	REACTOME: GUK1
	ConsensusPathDB
	Pathway Commons: GUK1
Metabolism	MetaCyc: GUK1
	HUMANCyc: GUK1
Regulation	Ensembl's Regulation: ENSG00000143774
	miRBase: chr1 :228,327,928-228,336,655
	TargetScan: NM_000858
	cisRED: ENSG00000143774
Context	iHOP: GUK1
	cancer metabolism search in PubMed: GUK1
	UCL Cancer Institute: GUK1
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for GUK1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GUK1
	Familial Cancer Database: GUK1

* 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_PURINE_METABOLISM REACTOME_ABACAVIR_TRANSPORT_AND_METABOLISM REACTOME_METABOLISM_OF_NUCLEOTIDES

Others
OMIM	139270; gene.
Orphanet
Disease	KEGG Disease: GUK1
	MedGen: GUK1 (Human Medical Genetics with Condition)
	ClinVar: GUK1
Phenotype	MGI: GUK1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GUK1

Mutations for GUK1

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GUK1 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
DA131615	GUK1	1	65	1	228328003	228328067	ARF1	62	629	1	228284778	228285698
BM827801	GUK1	1	218	1	228328004	228333769	ARFGAP1	216	329	20	61916216	61917060
BF987582	GUK1	1	111	1	228333478	228333590	GUK1	105	356	1	228332908	228333159
BU676367	GUK1	14	64	1	228336597	228336647	RP9	64	594	7	33134577	33136167
BE939838	GUK1	14	149	1	228335219	228336098	KDM5C	141	285	X	53228198	53228342
BI051269	GUK1	1	258	1	228336090	228336555	SMARCC1	243	389	3	47632258	47651631
BG742639	GUK1	1	498	1	228333052	228333551	FADS2	492	907	11	61634285	61634704
BQ012719	GUK1	18	120	1	228336550	228336652	CGA	115	444	6	87795223	87795552
BF766114	GUK1	1	184	1	228335348	228336409	GUK1	177	383	1	228328849	228333277
CF529503	GUK1	18	120	1	228336550	228336652	CGA	115	444	6	87795223	87795552

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

There's no copy number variation information in COSMIC data for this gene.

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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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=12)	Stat. for Synonymous SNVs (# total SNVs=8)

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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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
chr1:228334611-228334611	p.E75K	2
chr1:228334618-228334618	p.S77L	2
chr1:228335144-228335144	p.I97F	2
chr1:228335203-228335203	p.R116R	1
chr1:228335209-228335209	p.I118M	1
chr1:228335217-228335217	p.S121F	1
chr1:228335125-228335125	p.A90A	1
chr1:228335335-228335335	p.R137P	1
chr1:228333221-228333221	p.G3A	1
chr1:228335126-228335126	p.V91M	1

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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=2

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		1										4	1				3	4	1	7
# mutation		1										4	1				3	4	1	8
nonsynonymous SNV												2	1				2	3	1	6
synonymous SNV		1										2					1	1		2

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
chr1:228334611	p.E96K,GUK1	2
chr1:228336130	p.D122E,GUK1	1
chr1:228335126	p.T134T,GUK1	1
chr1:228336153	p.R137Q,GUK1	1
chr1:228335132	p.R137R,GUK1	1
chr1:228336392	p.R158P,GUK1	1
chr1:228335142	p.G24A,GUK1	1
chr1:228333221	p.S165I,GUK1	1
chr1:228335158	p.S31S,GUK1	1
chr1:228333243	p.R169R,GUK1	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 GUK1 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 GUK1

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


ARL6IP4,AURKAIP1,BCL7C,TSR3,C19orf24,C1orf35,C7orf50, C9orf142,C9orf16,FASTK,GUK1,LSM7,MRPL55,LINC00116, NDUFA11,NDUFB7,NDUFS6,NDUFS7,PRDX5,TMUB1,ZNHIT1	BAD,LAMTOR4,CCDC124,CHMP2A,DPM3,FAM195B,FKBP8, GNB2,GUK1,JMJD8,JOSD2,MBD3,MPG,MRPL28, RABAC1,ROMO1,RPS19BP1,SCAND1,SSNA1,TBCB,ZNHIT1

ARF1,ATP6V0B,AURKAIP1,COX7A2,DPM3,GUK1,HAX1, JTB,KRTCAP2,NAA38,MPG,MRPL54,MRPL55,MTX1, PSMB4,LAMTOR2,S100A6,SCO2,TMEM183A,TMEM219,TSPO	COX14,IFT43,SZRD1,DYNLT1,GUK1,MYEOV2,NDUFA13, NDUFA7,NDUFB7,POLR2F,PSENEN,PSMB1,PSMB4,PSMD8, PSMD9,RNF181,SCNM1,SNX17,TRAPPC3,UBL5,UQCR11

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 GUK1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	ChEMBL	CHEMBL4989; -.
Organism-specific databases	PharmGKB	PA29072; -.
Organism-specific databases	CTD	2987; -.

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
DB01972	guanylate kinase 1	experimental	Guanosine-5'-Monophosphate
DB03431	guanylate kinase 1	experimental	Adenosine-5'-Diphosphate
DB01942	guanylate kinase 1	experimental	Formic Acid
DB00130	guanylate kinase 1	approved; nutraceutical; investigational	L-Glutamine

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Cross referenced IDs for GUK1

* 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