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 ADK

Basic gene info.	Gene symbol	ADK
	Gene name	adenosine kinase
	Synonyms	AK
	Cytomap	UCSC genome browser: 10q22\|10q11-q24
	Genomic location	chr10 :75910942-76469061
	Type of gene	protein-coding
	RefGenes	NM_001123.3, NM_001202449.1,NM_001202450.1,NM_006721.3,
	Ensembl id	ENSG00000156110
	Description	adenosine 5'-phosphotransferase
	Modification date	20141207
dbXrefs	MIM : 102750
	HGNC : HGNC
	Ensembl : ENSG00000156110
	HPRD : 00039
	Vega : OTTHUMG00000018506
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ADK
	BioGPS: 132
	Gene Expression Atlas: ENSG00000156110
	The Human Protein Atlas: ENSG00000156110
Pathway	NCI Pathway Interaction Database: ADK
	KEGG: ADK
	REACTOME: ADK
	ConsensusPathDB
	Pathway Commons: ADK
Metabolism	MetaCyc: ADK
	HUMANCyc: ADK
Regulation	Ensembl's Regulation: ENSG00000156110
	miRBase: chr10 :75,910,942-76,469,061
	TargetScan: NM_001123
	cisRED: ENSG00000156110
Context	iHOP: ADK
	cancer metabolism search in PubMed: ADK
	UCL Cancer Institute: ADK
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: ADK
	Familial Cancer Database: ADK

* 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_METABOLISM_OF_NUCLEOTIDES REACTOME_PURINE_METABOLISM

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

Mutations for ADK

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- 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
breast	ADK	chr10	76003163	76003163		chr10	83183085	83183085
ovary	ADK	chr10	75998081	75998101		chr10	77199035	77199055
ovary	ADK	chr10	76011398	76011418	ADK	chr10	76013015	76013035
ovary	ADK	chr10	76187014	76187034	ADK	chr10	76188638	76188658
ovary	ADK	chr10	76278553	76278573	ADK	chr10	76415647	76415667
ovary	ADK	chr10	76317249	76317269		chr19	30181010	30181030
ovary	ADK	chr10	76398877	76398897		chr20	19724153	19724173
ovary	ADK	chr10	76398895	76398915		chr20	19729039	19729059
ovary	ADK	chr10	76447425	76447445	ADK	chr10	76442401	76442421
pancreas	ADK	chr10	76221770	76221790	ADK	chr10	76221712	76221732

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 ADK 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
BE699173	ADK	1	127	10	76153993	76158276	LSAMP	128	260	3	115918507	115918640
BM671160	ADK	53	394	10	76300474	76300815	ZNF644	390	424	1	91394007	91394181
AF092134	RWDD1	1	1072	6	116894039	116914431	ADK	1067	1087	10	75960241	75960261
BX098414	TRIP12	1	279	2	230702309	230702588	ADK	268	325	10	76101216	76101276

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	ns	ovary	pancre	prost	skin	stoma	thyro	urina
Total # sample	14		1	6			2		1		3		1	2	3		1
GAIN (# sample)	14			6			1				2				2
LOSS (# sample)			1				1		1		1		1	2	2		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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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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=17)	Stat. for Synonymous SNVs (# total SNVs=6)

Stat. for Deletions (# total SNVs=2)	Stat. for Insertions (# total SNVs=0)
	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
chr10:76429965-76429965	p.V301A	3
chr10:75960579-75960579	p.D41E	2
chr10:76468180-76468180	p.P356S	2
chr10:76429959-76429959	p.F299C	1
chr10:76074455-76074455	p.V75V	1
chr10:76158301-76158301	p.W173*	1
chr10:76074456-76074456	p.E76K	1
chr10:76158312-76158312	p.A179fs*6	1
chr10:76429966-76429966	p.V301V	1
chr10:76074471-76074471	p.G81S	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=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	2		1	6			1			1							5	2		6
# mutation	2		1	4			1			1							4	2		6
nonsynonymous SNV	2		1	3			1			1							2	2		2
synonymous SNV				1													2			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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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
chr10:76429965	p.V266A,ADK	3
chr10:76468180	p.P321S,ADK	2
chr10:76153949	p.I109I,ADK	1
chr10:76153970	p.K128T,ADK	1
chr10:76430010	p.E170K,ADK	1
chr10:76154057	p.A210V,ADK	1
chr10:76468112	p.R214T,ADK	1
chr10:76158270	p.G217G,ADK	1
chr10:75911080	p.V244M,ADK	1
chr10:76285071	p.V15A,ADK	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 ADK 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 ADK

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


ADK,ANAPC16,ANXA7,AP3M1,ASCC1,CAMK2G,MICU1, MCU,CHCHD1,DNAJC9,ECD,FAM149B1,LOC100128292,MRPS16, P4HA1,PCBD1,PPA1,RPS24,SEC24C,VCL,VDAC2	ADK,AIG1,ALG14,DTD2,TMEM230,CYB5B,DCTN6, FAM173B,FAM45A,HIGD1A,HNMT,ISCA1,LYRM1,METTL5, MOCS2,RNF11,RNF14,STRAP,TMEM218,UBE2E2,VPS29

ADK,PARPBP,CMSS1,CCDC58,CMC1,DBI,DPY30, ECD,HSPE1,MEMO1,MRPL48,MRPS16,MRPS23,NDUFAF2, PNO1,SNRPG,TFAM,TRUB1,WDR12,YWHAQ,ZC3H15	ADK,BOLA3,CENPK,CKS1B,COQ3,DAP3,EXOSC8, HSPE1,LSM3,LSM5,NHP2,NUP37,PPIA,PPIH, RAN,RFC2,RFC4,SNRNP40,SNRPD1,SNRPE,SSBP1

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 ADK

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
DB00131	adenosine kinase	approved; nutraceutical	Adenosine monophosphate
DB00811	adenosine kinase	approved	Ribavirin
DB07173	adenosine kinase	experimental	7-(5-DEOXY-BETA-D-RIBOFURANOSYL)-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-4-AMINE
DB07280	adenosine kinase	experimental	5-[4-(DIMETHYLAMINO)PHENYL]-6-[(6-MORPHOLIN-4-YLPYRIDIN-3-YL)ETHYNYL]PYRIMIDIN-4-AMINE
DB00173	adenosine kinase	approved; nutraceutical	Adenine
DB00640	adenosine kinase	approved; investigational	Adenosine

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Cross referenced IDs for ADK

* 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