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 MAT2A

Basic gene info.	Gene symbol	MAT2A
	Gene name	methionine adenosyltransferase II, alpha
	Synonyms	MATA2\|MATII\|SAMS2
	Cytomap	UCSC genome browser: 2p11.2
	Genomic location	chr2 :85766100-85772403
	Type of gene	protein-coding
	RefGenes	NM_005911.5,
	Ensembl id	ENSG00000168906
	Description	MAT 2MAT-IIS-adenosylmethionine synthase isoform type-2adoMet synthase 2adoMet synthetase 2methionine adenosyltransferase 2
	Modification date	20141207
dbXrefs	MIM : 601468
	HGNC : HGNC
	Ensembl : ENSG00000168906
	HPRD : 03275
	Vega : OTTHUMG00000130174
Protein	UniProt: P31153 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MAT2A
	BioGPS: 4144
	Gene Expression Atlas: ENSG00000168906
	The Human Protein Atlas: ENSG00000168906
Pathway	NCI Pathway Interaction Database: MAT2A
	KEGG: MAT2A
	REACTOME: MAT2A
	ConsensusPathDB
	Pathway Commons: MAT2A
Metabolism	MetaCyc: MAT2A
	HUMANCyc: MAT2A
Regulation	Ensembl's Regulation: ENSG00000168906
	miRBase: chr2 :85,766,100-85,772,403
	TargetScan: NM_005911
	cisRED: ENSG00000168906
Context	iHOP: MAT2A
	cancer metabolism search in PubMed: MAT2A
	UCL Cancer Institute: MAT2A
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for MAT2A(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: MAT2A
	Familial Cancer Database: MAT2A

* 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 KEGG_SELENOAMINO_ACID_METABOLISM REACTOME_SULFUR_AMINO_ACID_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

Others
OMIM	601468; gene.
Orphanet
Disease	KEGG Disease: MAT2A
	MedGen: MAT2A (Human Medical Genetics with Condition)
	ClinVar: MAT2A
Phenotype	MGI: MAT2A (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: MAT2A

Mutations for MAT2A

* 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	MAT2A	chr2	85766957	85766977	MAT2A	chr2	85768960	85768980
ovary	MAT2A	chr2	85767414	85767434	MAT2A	chr2	85768802	85768822

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 MAT2A 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
BM823880	PARP15	95	117	3	122305561	122305587	MAT2A	115	359	2	85769284	85769718
BM749134	MAT2A	14	119	2	85766291	85766396	CNOT7	116	538	8	17100571	17104270
BG329301	MAT2A	2	56	2	85771460	85771514	UBE2O	54	721	17	74387226	74388123
BP362529	MAT2A	1	415	2	85769395	85770157	CNTN2	413	582	1	205036226	205038635
AA992625	ADAMTSL4	12	321	1	150533101	150533409	MAT2A	308	429	2	85769031	85769334
BG620787	MAT2A	1	463	2	85767606	85768067	CYP19A1	445	549	15	51501673	51501777
BF746473	MAT2A	19	121	2	85771560	85771663	GSS	119	244	20	33533756	33533881

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=22)	Stat. for Synonymous SNVs (# total SNVs=11)

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
chr2:85769711-85769711	p.R264R	3
chr2:85768427-85768427	p.S73S	1
chr2:85769862-85769862	p.L315V	1
chr2:85769075-85769075	p.R177C	1
chr2:85770792-85770792	p.?	1
chr2:85769496-85769496	p.Q256H	1
chr2:85768459-85768459	p.R84H	1
chr2:85769871-85769871	p.?	1
chr2:85769271-85769271	p.?	1
chr2:85770889-85770889	p.K394K	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	3		2			3		3	1		2	1	1			4	3		2
# mutation	5	3		2			3		3	1		2	1	1			4	3		2
nonsynonymous SNV	5	1		2			3		1	1		1	1	1			2			2
synonymous SNV		2							2			1					2	3

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
chr2:85768989	p.A162V	1
chr2:85769770	p.I330V	1
chr2:85770125	p.A165A	1
chr2:85769031	p.F333F	1
chr2:85769804	p.R177C	1
chr2:85770138	p.K340M	1
chr2:85769041	p.R177H	1
chr2:85769823	p.E342K	1
chr2:85770889	p.E217E	1
chr2:85769075	p.E344Q	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 MAT2A 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 MAT2A

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


C16orf52,C1orf220,CCDC125,FAM13B,CLUHP3,KIF3A,MAT2A, PAN2,PCBD2,PWWP2A,REV1,SECISBP2,SREK1,SRRM2, TNRC6A,TRIM52,TRIM66,TTC14,CFAP44,YTHDC2,ZBTB26	AMD1,AP1S3,ARF6,CDC42SE1,CDK2,CRY1,DDX5, FZD3,MACC1,MAK,MAT2A,NIP7,PNO1,PPP4R1, RBM12,SLC20A1,SPAG1,TMEM185B,UBXN10,WEE1,ZNF35

DDX39B,DDX12P,DDX55,DUSP28,EXOSC2,GEN1,GPR75, HJURP,KIAA0907,KNTC1,LOC440944,LOC642846,MAT2A,NR2C1, SRSF2,SRSF6,SRSF7,SNHG1,SNHG3,SNHG4,TCERG1	AEN,C1orf100,C6orf141,DDX21,DNAJC2,EFNB2,ETF1, FOSL1,GPR3,MARS2,MAT2A,PDE12,PIGW,PLEKHG1, SEH1L,TNFRSF12A,TRMT6,URB2,UTP15,XIRP1,ZNF562

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 MAT2A

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA30647; -.
Organism-specific databases	CTD	4144; -.

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
DB00118	methionine adenosyltransferase II, alpha	approved; nutraceutical	S-Adenosylmethionine

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Cross referenced IDs for MAT2A

* 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