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 MARS

Basic gene info.	Gene symbol	MARS
	Gene name	methionyl-tRNA synthetase
	Synonyms	METRS\|MRS\|MTRNS\|SPG70
	Cytomap	UCSC genome browser: 12q13.3
	Genomic location	chr12 :57881735-57910438
	Type of gene	protein-coding
	RefGenes	NM_004990.3,
	Ensembl id	ENSG00000166986
	Description	cytosolic methionyl-tRNA synthetasemethionine--tRNA ligase, cytoplasmic
	Modification date	20141212
dbXrefs	MIM : 156560
	HGNC : HGNC
	Ensembl : ENSG00000166986
	HPRD : 08864
	Vega : OTTHUMG00000169996
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MARS
	BioGPS: 4141
	Gene Expression Atlas: ENSG00000166986
	The Human Protein Atlas: ENSG00000166986
Pathway	NCI Pathway Interaction Database: MARS
	KEGG: MARS
	REACTOME: MARS
	ConsensusPathDB
	Pathway Commons: MARS
Metabolism	MetaCyc: MARS
	HUMANCyc: MARS
Regulation	Ensembl's Regulation: ENSG00000166986
	miRBase: chr12 :57,881,735-57,910,438
	TargetScan: NM_004990
	cisRED: ENSG00000166986
Context	iHOP: MARS
	cancer metabolism search in PubMed: MARS
	UCL Cancer Institute: MARS
Assigned class in ccmGDB	C

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

Cancer 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/

Metabolic Pathway Description
KEGG_SELENOAMINO_ACID_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: MARS
	MedGen: MARS (Human Medical Genetics with Condition)
	ClinVar: MARS
Phenotype	MGI: MARS (International Mouse Phenotyping Consortium)
Phenotype	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.

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

There's no intra-chromosomal structural variation.

Sample

Symbol_a

Chr_a

Start_a

End_a

Symbol_b

Chr_b

Start_b

End_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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MARS 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
AJ301612	FUS	1	118	16	31193868	31193985	MARS	119	225	12	57911163	57911536
X92120	EWSR1	1	262	22	29678497	29683123	MARS	263	883	12	57910561	57911536
AW409902	ARHGAP9	27	446	12	57881880	57883307	MARS	443	466	12	57883303	57883326
S75763	FUS	1	271	16	31195241	31195717	MARS	270	377	12	57911164	57911538
BE269882	ARHGAP9	1	409	12	57881899	57883307	MARS	406	429	12	57883303	57883326
AA345023	FBRSL1	58	108	12	133147653	133147703	MARS	102	227	12	57909054	57909762
BE295899	ARHGAP9	1	404	12	57881899	57883307	MARS	401	424	12	57883303	57883326
BC001814	MARS	426	449	12	57883303	57883326	EIF3L	450	2327	22	38245441	38284638
AW410123	MARS	18	308	12	57894237	57905627	MARS	303	453	12	57905855	57906137

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=4

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Somatic 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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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
chr12:57883053-57883053	p.L71fs*33	4
chr12:57892036-57892036	p.L289L	3
chr12:57883298-57883298	p.I124T	3
chr12:57906098-57906098	p.E572V	3
chr12:57906610-57906610	p.T610T	2
chr12:57910042-57910042	p.P826P	2
chr12:57908816-57908816	p.R727W	2
chr12:57905648-57905648	p.D512E	2
chr12:57894178-57894178	p.C389Y	2
chr12:57908817-57908817	p.R727Q	2

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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		2		12	1		2		3	1		4	3	2			9	4	1	14
# mutation		2		13	1		2		3	1		4	3	2			9	4	1	15
nonsynonymous SNV		2		10	1		2		2	1		2	1	2			4	3	1	11
synonymous SNV				3					1			2	2				5	1		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
chr12:57906610	p.G730D	2
chr12:57908826	p.T610T	2
chr12:57910042	p.P826P	2
chr12:57894268	p.R399H	1
chr12:57910304	p.P626H	1
chr12:57883717	p.A844V	1
chr12:57891963	p.T188I	1
chr12:57908816	p.V401M	1
chr12:57894286	p.L650P	1
chr12:57910320	p.V856V	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 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

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


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

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 MARS

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
DB00145	methionyl-tRNA synthetase	approved; nutraceutical	Glycine
DB00160	methionyl-tRNA synthetase	approved; nutraceutical	L-Alanine
DB00125	methionyl-tRNA synthetase	approved; nutraceutical	L-Arginine
DB00151	methionyl-tRNA synthetase	approved; nutraceutical	L-Cysteine
DB00130	methionyl-tRNA synthetase	approved; nutraceutical; investigational	L-Glutamine
DB00117	methionyl-tRNA synthetase	approved; nutraceutical	L-Histidine
DB00149	methionyl-tRNA synthetase	approved; nutraceutical	L-Leucine
DB00123	methionyl-tRNA synthetase	approved; nutraceutical	L-Lysine
DB00134	methionyl-tRNA synthetase	approved; nutraceutical	L-Methionine
DB00120	methionyl-tRNA synthetase	approved; nutraceutical	L-Phenylalanine
DB00172	methionyl-tRNA synthetase	approved; nutraceutical	L-Proline
DB00133	methionyl-tRNA synthetase	approved; nutraceutical	L-Serine
DB00156	methionyl-tRNA synthetase	approved; nutraceutical	L-Threonine
DB00150	methionyl-tRNA synthetase	approved; nutraceutical	L-Tryptophan
DB00135	methionyl-tRNA synthetase	approved; nutraceutical	L-Tyrosine
DB00161	methionyl-tRNA synthetase	approved; nutraceutical	L-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