Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolMAT2A
Gene namemethionine adenosyltransferase II, alpha
SynonymsMATA2|MATII|SAMS2
CytomapUCSC genome browser: 2p11.2
Genomic locationchr2 :85766100-85772403
Type of geneprotein-coding
RefGenesNM_005911.5,
Ensembl idENSG00000168906
DescriptionMAT 2MAT-IIS-adenosylmethionine synthase isoform type-2adoMet synthase 2adoMet synthetase 2methionine adenosyltransferase 2
Modification date20141207
dbXrefs MIM : 601468
HGNC : HGNC
Ensembl : ENSG00000168906
HPRD : 03275
Vega : OTTHUMG00000130174
ProteinUniProt: P31153
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MAT2A
BioGPS: 4144
Gene Expression Atlas: ENSG00000168906
The Human Protein Atlas: ENSG00000168906
PathwayNCI Pathway Interaction Database: MAT2A
KEGG: MAT2A
REACTOME: MAT2A
ConsensusPathDB
Pathway Commons: MAT2A
MetabolismMetaCyc: MAT2A
HUMANCyc: MAT2A
RegulationEnsembl's Regulation: ENSG00000168906
miRBase: chr2 :85,766,100-85,772,403
TargetScan: NM_005911
cisRED: ENSG00000168906
ContextiHOP: MAT2A
cancer metabolism search in PubMed: MAT2A
UCL Cancer Institute: MAT2A
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for MAT2A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM
KEGG_SELENOAMINO_ACID_METABOLISM
REACTOME_SULFUR_AMINO_ACID_METABOLISM
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

check002.gifOthers
OMIM 601468; gene.
Orphanet
DiseaseKEGG Disease: MAT2A
MedGen: MAT2A (Human Medical Genetics with Condition)
ClinVar: MAT2A
PhenotypeMGI: MAT2A (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryMAT2Achr28576695785766977MAT2Achr28576896085768980
ovaryMAT2Achr28576741485767434MAT2Achr28576880285768822
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MAT2A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BM823880PARP15951173122305561122305587MAT2A11535928576928485769718
BM749134MAT2A1411928576629185766396CNOT711653881710057117104270
BG329301MAT2A25628577146085771514UBE2O54721177438722674388123
BP362529MAT2A141528576939585770157CNTN24135821205036226205038635
AA992625ADAMTSL4123211150533101150533409MAT2A30842928576903185769334
BG620787MAT2A146328576760685768067CYP19A1445549155150167351501777
BF746473MAT2A1912128577156085771663GSS119244203353375633533881

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy 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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr2:85769711-85769711p.R264R3
chr2:85768223-85768223p.I37L1
chr2:85769735-85769736p.W274fs*341
chr2:85768962-85768962p.F139S1
chr2:85770091-85770091p.K340M1
chr2:85769398-85769398p.E224K1
chr2:85768229-85768229p.D39H1
chr2:85769744-85769744p.G275G1
chr2:85768975-85768975p.T143T1
chr2:85770096-85770096p.E342K1

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample13 2  3 31 211  43 2
# mutation53 2  3 31 211  43 2
nonsynonymous SNV51 2  3 11 111  2  2
synonymous SNV 2      2  1    23  
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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr2:85768223p.A55D1
chr2:85769379p.G284E1
chr2:85770052p.E111Q1
chr2:85768278p.A295A1
chr2:85769398p.D129Y1
chr2:85770060p.A302T1
chr2:85768794p.F139S1
chr2:85769496p.S304S1
chr2:85770071p.T143T1
chr2:85768848p.L315V1

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA30647; -.
Organism-specific databasesCTD 4144; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00118methionine adenosyltransferase II, alphaapproved; nutraceuticalS-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



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