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 MTAP

Basic gene info.	Gene symbol	MTAP
	Gene name	methylthioadenosine phosphorylase
	Synonyms	BDMF\|DMSFH\|DMSMFH\|HEL-249\|LGMBF\|MSAP\|c86fus
	Cytomap	UCSC genome browser: 9p21
	Genomic location	chr9 :21802634-21865969
	Type of gene	protein-coding
	RefGenes	NM_002451.3,
	Ensembl id	ENSG00000099810
	Description	5'-methylthioadenosine phosphorylaseMTA phosphorylaseMTAPaseMeSAdo phosphorylaseS-methyl-5'-thioadenosine phosphorylaseepididymis luminal protein 249
	Modification date	20141207
dbXrefs	MIM : 156540
	HGNC : HGNC
	Ensembl : ENSG00000099810
	HPRD : 01134
	Vega : OTTHUMG00000019690
Protein	UniProt: Q13126 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MTAP
	BioGPS: 4507
	Gene Expression Atlas: ENSG00000099810
	The Human Protein Atlas: ENSG00000099810
Pathway	NCI Pathway Interaction Database: MTAP
	KEGG: MTAP
	REACTOME: MTAP
	ConsensusPathDB
	Pathway Commons: MTAP
Metabolism	MetaCyc: MTAP
	HUMANCyc: MTAP
Regulation	Ensembl's Regulation: ENSG00000099810
	miRBase: chr9 :21,802,634-21,865,969
	TargetScan: NM_002451
	cisRED: ENSG00000099810
Context	iHOP: MTAP
	cancer metabolism search in PubMed: MTAP
	UCL Cancer Institute: MTAP
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of MTAP in cancer cell metabolism	1. Shlomi T, Fan J, Tang B, Kruger WD, Rabinowitz JD (2014) Quantitation of cellular metabolic fluxes of methionine. Analytical chemistry 86: 1583-1591. go to article 2. Munshi PN, Lubin M, Bertino JR (2014) 6-Thioguanine: A drug with unrealized potential for cancer therapy. The oncologist: theoncologist. 2014-0178. go to article

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

Cancer Description
Cancer	CGAP: MTAP
	Familial Cancer Database: MTAP

* 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_CYSTEINE_AND_METHIONINE_METABOLISM REACTOME_SULFUR_AMINO_ACID_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES REACTOME_METABOLISM_OF_POLYAMINES

Others
OMIM	112250; phenotype. 112250; phenotype. 156540; gene. 156540; gene.
Orphanet	85182; Diaphyseal medullary stenosis - bone malignancy. 85182; Diaphyseal medullary stenosis - bone malignancy.
Disease	KEGG Disease: MTAP
	MedGen: MTAP (Human Medical Genetics with Condition)
	ClinVar: MTAP
Phenotype	MGI: MTAP (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: MTAP

Mutations for MTAP

* 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
haematopoietic_and_lymphoid_tissue	MTAP	chr9	21848957	21848957	MTAP	chr9	21848957	21848957
pancreas	MTAP	chr9	21802628	21802648		chr9	13766693	13766713
pancreas	MTAP	chr9	21803377	21803397	MTAP	chr9	21803677	21803697
pancreas	MTAP	chr9	21812289	21812309		chr9	22237408	22237428
pancreas	MTAP	chr9	21821029	21821049		chr9	22518205	22518225
pancreas	MTAP	chr9	21828665	21828685	MTAP	chr9	21829729	21829749
pancreas	MTAP	chr9	21828675	21828695	MTAP	chr9	21829912	21829932
pancreas	MTAP	chr9	21829139	21829159		chr9	22572342	22572362
pancreas	MTAP	chr9	21829732	21829752	MTAP	chr9	21829920	21829940
pancreas	MTAP	chr9	21833558	21833578	CDKN2B-AS1	chr9	22023490	22023510
pancreas	MTAP	chr9	21840363	21840363		chr9	22834629	22834629
pancreas	MTAP	chr9	21842693	21842713	CDKN2B-AS1	chr9	22047646	22047666
pancreas	MTAP	chr9	21849319	21849319	ELAVL2	chr9	23745195	23745195
pancreas	MTAP	chr9	21851148	21851168	CDKN2B-AS1	chr9	22076414	22076434
pancreas	MTAP	chr9	21855379	21855399		chr9	25852755	25852775
pancreas	MTAP	chr9	21860741	21860761	CDKN2B-AS1	chr9	22026721	22026741
pancreas	MTAP	chr9	21864488	21864508		chr9	22320545	22320565
pancreas	MTAP	chr9	21865657	21865677	CDKN2B-AS1	chr9	22085313	22085333
skin	MTAP	chr9	21810667	21810667	FLJ35282	chr9	22697036	22697036

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 MTAP 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
CN365873	MTAP	1	110	9	21970908	21971017	MTAP	105	167	9	21974715	21974777
CR738223	UPF2	1	61	10	12011461	12011521	MTAP	55	220	9	21861026	21861193

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	5	29		1		1			14		1			14	4		12
GAIN (# sample)	1										1
LOSS (# sample)	4	29		1		1			14					14	4		12

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=14)	Stat. for Synonymous SNVs (# total SNVs=9)

Stat. for Deletions (# total SNVs=1)	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
chr9:21816739-21816739	p.K49K	3
chr9:21837988-21837988	p.P143P	2
chr9:21816750-21816750	p.V53A	1
chr9:21854633-21854633	p.L152F	1
chr9:21859391-21859391	p.S260S	1
chr9:21816758-21816758	p.V56I	1
chr9:21854687-21854687	p.V170I	1
chr9:21859395-21859395	p.E262K	1
chr9:21816760-21816760	p.V56V	1
chr9:21854695-21854695	p.I172I	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		1			2		3			1	2				5	1		7
# mutation		1		1			2		3			1	2				7	1		8
nonsynonymous SNV		1					2		2				2				4	1		4
synonymous SNV				1					1			1					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
chr9:21837988	p.P143P	2
chr9:21818104	p.L152F	1
chr9:21854712	p.V170I	1
chr9:21818193	p.I172I	1
chr9:21854722	p.R176H	1
chr9:21837927	p.S178N	1
chr9:21854770	p.G48W	1
chr9:21837965	p.A181A	1
chr9:21854777	p.K49K	1
chr9:21837985	p.T197T	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 MTAP 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 MTAP

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


CDKN2A-AS1,CAAP1,CDKN2A,FAM136A,HAUS6,KIAA0020,FOCAD, KLHL9,MELK,MTAP,NFIB,PLAA,POLR1E,PRKX, RCL1,SERBP1,SUV39H2,SYNCRIP,TEX10,TOMM5,UHRF2	GOPC,JRKL,KIAA1804,KLHL9,MBLAC2,MBTD1,MTAP, NFXL1,PAN3,PHF6,PUM2,SASS6,SPIN4,SUDS3, SUV420H1,TRIM2,USP1,ZBTB33,ZNF12,ZNF84,ZZZ3

APTX,CHORDC1,DNAJA1,EXOSC3,HAUS6,KIAA0020,LOC727896, SLC25A51,MTAP,NCL,NOL6,POLR1E,PSIP1,QSOX2, RCL1,SET,SIGMAR1,SMU1,STIP1,UBAP2,ZCCHC7	AP3M1,ARMCX3,KANSL1L,C3orf58,DDX19A,DHX57,EIF5B, GEMIN5,HLTF,IPO7,CFAP97,LOC221710,LRRC58,MTAP, MYEF2,NEDD1,NUCKS1,JADE3,PHF20,TOMM70A,ZMYM4

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 MTAP

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	Q13126; -.
Chemistry	ChEMBL	CHEMBL4941; -.
Chemistry	BindingDB	Q13126; -.
Chemistry	ChEMBL	CHEMBL4941; -.
Organism-specific databases	PharmGKB	PA31220; -.
Organism-specific databases	PharmGKB	PA31220; -.
Organism-specific databases	CTD	4507; -.
Organism-specific databases	CTD	4507; -.

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
DB00173	methylthioadenosine phosphorylase	approved; nutraceutical	Adenine
DB02158	methylthioadenosine phosphorylase	experimental	(1s)-1-(9-Deazaadenin-9-Yl)-1,4,5-Trideoxy-1,4-Imino-5-Methylthio-D-Ribitol
DB02281	methylthioadenosine phosphorylase	experimental	Formycin
DB02282	methylthioadenosine phosphorylase	experimental	5'-Deoxy-5'-Methylthioadenosine
DB02933	methylthioadenosine phosphorylase	experimental	5'-Deoxy-5'-(Methylthio)-Tubercidin

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Cross referenced IDs for MTAP

* 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