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 ADA

Basic gene info.	Gene symbol	ADA
	Gene name	adenosine deaminase
	Synonyms	-
	Cytomap	UCSC genome browser: 20q13.12
	Genomic location	chr20 :43248162-43280376
	Type of gene	protein-coding
	RefGenes	NM_000022.2,
	Ensembl id	ENSG00000196839
	Description	adenosine aminohydrolase
	Modification date	20141221
dbXrefs	MIM : 608958
	HGNC : HGNC
	Ensembl : ENSG00000196839
	HPRD : 00038
	Vega : OTTHUMG00000033081
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ADA
	BioGPS: 100
	Gene Expression Atlas: ENSG00000196839
	The Human Protein Atlas: ENSG00000196839
Pathway	NCI Pathway Interaction Database: ADA
	KEGG: ADA
	REACTOME: ADA
	ConsensusPathDB
	Pathway Commons: ADA
Metabolism	MetaCyc: ADA
	HUMANCyc: ADA
Regulation	Ensembl's Regulation: ENSG00000196839
	miRBase: chr20 :43,248,162-43,280,376
	TargetScan: NM_000022
	cisRED: ENSG00000196839
Context	iHOP: ADA
	cancer metabolism search in PubMed: ADA
	UCL Cancer Institute: ADA
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: ADA
	Familial Cancer Database: ADA

* 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: ADA
	MedGen: ADA (Human Medical Genetics with Condition)
	ClinVar: ADA
Phenotype	MGI: ADA (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ADA

Mutations for ADA

* 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
ovary	ADA	chr20	43254899	43254919	ADA	chr20	43255058	43255078
pancreas	ADA	chr20	43273246	43273266	ZSWIM3	chr20	44488405	44488425

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 ADA related fusion information.

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

AW085123

KIAA0430

172

201

15705035

15705064

ADA

182

204

43266946

43266968

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=21)	Stat. for Synonymous SNVs (# total SNVs=14)

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
chr20:43251662-43251662	p.E222K	3
chr20:43257798-43257798	p.I36I	3
chr20:43280227-43280227	p.D8N	3
chr20:43248488-43248488	p.G360E	2
chr20:43264866-43264866	p.?	2
chr20:43251728-43251728	p.?	2
chr20:43255177-43255177	p.G94G	2
chr20:43251493-43251493	p.R253W	2
chr20:43254263-43254263	p.R142Q	1
chr20:43249764-43249764	p.Y290Y	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	1	3		6			2		1	1		4		1		1	3	7		5
# mutation	1	3		7			2		1	1		4		1		1	3	7		5
nonsynonymous SNV		2		5			1			1		2		1		1	1	4		1
synonymous SNV	1	1		3			1		1			2					2	3		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
chr20:43257798	p.I36I	3
chr20:43255112	p.L252M	2
chr20:43251496	p.E222K	2
chr20:43251662	p.P116H	2
chr20:43249743	p.R282W	1
chr20:43252921	p.C75C	1
chr20:43257807	p.G270V	1
chr20:43249764	p.A73T	1
chr20:43252948	p.F259F	1
chr20:43248478	p.D53Y	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 ADA 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 ADA

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


ADAL,CASC4,PRIMPOL,CSNK1G3,DCTN4,IQCH,LCMT2, MFAP1,FAN1,MYO5C,BLOC1S6,PPIP5K1,RFX7,RTF1, SPG11,TP53BP1,TUBGCP4,UBE3A,UBR1,VPS39,ZSCAN29	ACAT1,ADAL,ATPAF1,DLD,ETFDH,MTFR1L,HADHB, KLHL31,NDUFS1,NNT,NRD1,PARK2,PDHX,PHYH, PPP3CB,RRAGD,SOX6,SUCLA2,UBR3,ZAK,ZYG11B

ADAL,AQR,DPH6,VWA9,COPS2,EIF2AK4,EIF3J, LCMT2,LRRC57,FAN1,NDNL2,PARP16,PDCD7,PEX12, RTF1,TRPM7,TUBGCP5,UBE3A,USP8,ZNF770,ZSCAN29	ABCA11P,ADAL,AIMP1,ATF1,BRIX1,C1orf109,C5orf28, TRMT13,FAM133B,GNL3,IMMP1L,ITGB3BP,GPALPP1,KRR1, NHP2L1,PIBF1,PRMT3,SNRNP27,TASP1,TMEM182,TRMT12

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 ADA

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
DB00552	adenosine deaminase	approved; investigational	Pentostatin
DB00975	adenosine deaminase	approved	Dipyridamole
DB02096	adenosine deaminase	experimental	FR221647
DB02472	adenosine deaminase	experimental	6-Hydroxy-7,8-Dihydro Purine Nucleoside
DB02616	adenosine deaminase	experimental	FR117016
DB02830	adenosine deaminase	experimental	FR236913
DB03015	adenosine deaminase	experimental	6-Hydroxy-1,6-Dihydro Purine Nucleoside
DB03220	adenosine deaminase	experimental	FR233623
DB03370	adenosine deaminase	experimental	FR239087
DB03572	adenosine deaminase	experimental	FR230513
DB04218	adenosine deaminase	experimental	1-Deaza-Adenosine
DB04440	adenosine deaminase	experimental	Purine Riboside
DB07711	adenosine deaminase	experimental	(2S,3R)-3-(6-amino-9H-purin-9-yl)nonan-2-ol
DB07783	adenosine deaminase	experimental	1-((1R)-1-(HYDROXYMETHYL)-3-{6-[(3-PHENYLPROPANOYL)AMINO]-1H-INDOL-1-YL}PROPYL)-1H-IMIDAZOLE-4-CARBOXAMIDE
DB07785	adenosine deaminase	experimental	1-{(1R,2S)-2-HYDROXY-1-[2-(2-NAPHTHYLOXY)ETHYL]PROPYL}-1H-IMIDAZONE-4-CARBOXAMIDE
DB07786	adenosine deaminase	experimental	1-((1R,2S)-1-{2-[2-(4-CHLOROPHENYL)-1,3-BENZOXAZOL-7-YL]ETHYL}-2-HYDROXYPROPYL)-1H-IMIDAZOLE-4-CARBOXAMIDE
DB00173	adenosine deaminase	approved; nutraceutical	Adenine
DB00563	adenosine deaminase	approved	Methotrexate
DB00640	adenosine deaminase	approved; investigational	Adenosine

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Cross referenced IDs for ADA

* 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