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 MARS
Basic gene info.Gene symbolMARS
Gene namemethionyl-tRNA synthetase
SynonymsMETRS|MRS|MTRNS|SPG70
CytomapUCSC genome browser: 12q13.3
Genomic locationchr12 :57881735-57910438
Type of geneprotein-coding
RefGenesNM_004990.3,
Ensembl idENSG00000166986
Descriptioncytosolic methionyl-tRNA synthetasemethionine--tRNA ligase, cytoplasmic
Modification date20141212
dbXrefs MIM : 156560
HGNC : HGNC
Ensembl : ENSG00000166986
HPRD : 08864
Vega : OTTHUMG00000169996
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MARS
BioGPS: 4141
Gene Expression Atlas: ENSG00000166986
The Human Protein Atlas: ENSG00000166986
PathwayNCI Pathway Interaction Database: MARS
KEGG: MARS
REACTOME: MARS
ConsensusPathDB
Pathway Commons: MARS
MetabolismMetaCyc: MARS
HUMANCyc: MARS
RegulationEnsembl's Regulation: ENSG00000166986
miRBase: chr12 :57,881,735-57,910,438
TargetScan: NM_004990
cisRED: ENSG00000166986
ContextiHOP: MARS
cancer metabolism search in PubMed: MARS
UCL Cancer Institute: MARS
Assigned class in ccmGDBC

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Phenotypic Information for MARS(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MARS
Familial Cancer Database: MARS
* 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_SELENOAMINO_ACID_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: MARS
MedGen: MARS (Human Medical Genetics with Condition)
ClinVar: MARS
PhenotypeMGI: MARS (International Mouse Phenotyping Consortium)
PhenomicDB: MARS

Mutations for MARS
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
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 MARS related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AJ301612FUS1118163119386831193985MARS119225125791116357911536
X92120EWSR11262222967849729683123MARS263883125791056157911536
AW409902ARHGAP927446125788188057883307MARS443466125788330357883326
S75763FUS1271163119524131195717MARS270377125791116457911538
BE269882ARHGAP91409125788189957883307MARS406429125788330357883326
AA345023FBRSL15810812133147653133147703MARS102227125790905457909762
BE295899ARHGAP91404125788189957883307MARS401424125788330357883326
BC001814MARS426449125788330357883326EIF3L4502327223824544138284638
AW410123MARS18308125789423757905627MARS303453125790585557906137

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample 6      1    12  
GAIN (# sample) 6      1    12  
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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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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=63)
Stat. for Synonymous SNVs
(# total SNVs=21)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=1)

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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
chr12:57883053-57883053p.L71fs*334
chr12:57892036-57892036p.L289L3
chr12:57883298-57883298p.I124T3
chr12:57906098-57906098p.E572V3
chr12:57906610-57906610p.T610T2
chr12:57910042-57910042p.P826P2
chr12:57908816-57908816p.R727W2
chr12:57905648-57905648p.D512E2
chr12:57894178-57894178p.C389Y2
chr12:57908817-57908817p.R727Q2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 2 121 2 31 432  94114
# mutation 2 131 2 31 432  94115
nonsynonymous SNV 2 101 2 21 212  43111
synonymous SNV   3    1  22   51 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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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
chr12:57906610p.G730D2
chr12:57908826p.T610T2
chr12:57910042p.P826P2
chr12:57894268p.R399H1
chr12:57910304p.P626H1
chr12:57883717p.A844V1
chr12:57891963p.T188I1
chr12:57908816p.V401M1
chr12:57894286p.L650P1
chr12:57910320p.V856V1

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 MARS 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 MARS

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

ASNSD1,COA7,DDX21,GTF3C3,HSPD1,LRPPRC,MARS2,
MOB4,NOLC1,NOP58,PNO1,POLR1B,PRPF40A,PUS7,
RQCD1,SF3B1,URB2,WDR12,WDR43,WDR75,ZC3H15
BEND3,DSC2,FAM60A,LARS,MARS2,MCM4,MTMR1,
NKRF,NOLC1,PAICS,POLR1B,PPAT,QTRTD1,SLC12A2,
SMARCC1,SRPK1,SSX2IP,TEX10,URB2,USP10,ZBED4

C2orf47,CEBPZ,DDX18,FASTKD1,FASTKD2,HSPD1,LRPPRC,
MARS2,METTL8,MRPL19,MRPL30,MTIF2,NOC3L,PNO1,
PNPT1,POLR1B,PTCD3,SCLY,WDR12,WDR43,WDR75
AEN,AGPAT5,BYSL,FAM210A,FUT4,GRPEL1,KCNN4,
MARS2,MECOM,PDE12,PIGW,PPIF,PUS1,RCL1,
RDH13,RRP1,SEH1L,SLC25A19,TAF5L,URB2,UTP15
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 MARS
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00145methionyl-tRNA synthetaseapproved; nutraceuticalGlycine
DB00160methionyl-tRNA synthetaseapproved; nutraceuticalL-Alanine
DB00125methionyl-tRNA synthetaseapproved; nutraceuticalL-Arginine
DB00151methionyl-tRNA synthetaseapproved; nutraceuticalL-Cysteine
DB00130methionyl-tRNA synthetaseapproved; nutraceutical; investigationalL-Glutamine
DB00117methionyl-tRNA synthetaseapproved; nutraceuticalL-Histidine
DB00149methionyl-tRNA synthetaseapproved; nutraceuticalL-Leucine
DB00123methionyl-tRNA synthetaseapproved; nutraceuticalL-Lysine
DB00134methionyl-tRNA synthetaseapproved; nutraceuticalL-Methionine
DB00120methionyl-tRNA synthetaseapproved; nutraceuticalL-Phenylalanine
DB00172methionyl-tRNA synthetaseapproved; nutraceuticalL-Proline
DB00133methionyl-tRNA synthetaseapproved; nutraceuticalL-Serine
DB00156methionyl-tRNA synthetaseapproved; nutraceuticalL-Threonine
DB00150methionyl-tRNA synthetaseapproved; nutraceuticalL-Tryptophan
DB00135methionyl-tRNA synthetaseapproved; nutraceuticalL-Tyrosine
DB00161methionyl-tRNA synthetaseapproved; nutraceuticalL-Valine


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Cross referenced IDs for MARS
* 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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