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 GATM

Basic gene info.	Gene symbol	GATM
	Gene name	glycine amidinotransferase (L-arginine:glycine amidinotransferase)
	Synonyms	AGAT\|AT\|CCDS3
	Cytomap	UCSC genome browser: 15q21.1
	Genomic location	chr15 :45653321-45670980
	Type of gene	protein-coding
	RefGenes	NM_001482.2,
	Ensembl id	ENSG00000171766
	Description	glycine amidinotransferase, mitochondrialtransamidinase
	Modification date	20141219
dbXrefs	MIM : 602360
	HGNC : HGNC
	Ensembl : ENSG00000171766
	HPRD : 03838
	Vega : OTTHUMG00000131427
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GATM
	BioGPS: 2628
	Gene Expression Atlas: ENSG00000171766
	The Human Protein Atlas: ENSG00000171766
Pathway	NCI Pathway Interaction Database: GATM
	KEGG: GATM
	REACTOME: GATM
	ConsensusPathDB
	Pathway Commons: GATM
Metabolism	MetaCyc: GATM
	HUMANCyc: GATM
Regulation	Ensembl's Regulation: ENSG00000171766
	miRBase: chr15 :45,653,321-45,670,980
	TargetScan: NM_001482
	cisRED: ENSG00000171766
Context	iHOP: GATM
	cancer metabolism search in PubMed: GATM
	UCL Cancer Institute: GATM
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: GATM
	Familial Cancer Database: GATM

* 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_GLYCINE_SERINE_AND_THREONINE_METABOLISM KEGG_ARGININE_AND_PROLINE_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

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

Mutations for GATM

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GATM 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
BF933512	GATM	4	194	15	45656269	45656463	DDX3X	187	379	X	41197147	41197339
AW861199	WSB1	11	190	17	25630423	25630602	GATM	177	196	15	45657895	45657914
BF946024	GATM	14	316	15	45653805	45654108	TSEN2	300	319	3	12560544	12560563

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=29)	Stat. for Synonymous SNVs (# total SNVs=5)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	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
chr15:45656164-45656164	p.L365V	2
chr15:45660378-45660378	p.R189C	2
chr15:45658338-45658338	p.S295F	1
chr15:45668891-45668891	p.V66I	1
chr15:45658700-45658700	p.P228S	1
chr15:45656125-45656125	p.P378S	1
chr15:45661613-45661613	p.N132T	1
chr15:45658353-45658353	p.R290K	1
chr15:45668979-45668979	p.F36L	1
chr15:45660331-45660331	p.F204F	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	4	1	3	2		2		2			6	2	1			5	4		6
# mutation	1	4	1	3	2		2		2			6	2	1			6	4		6
nonsynonymous SNV	1	4		2	2		2		2			6	1	1			4	3		5
synonymous SNV			1	1									1				2	1		1

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
chr15:45658607	p.D298Y	1
chr15:45660395	p.R187L	1
chr15:45657019	p.K297K	1
chr15:45669010	p.R187C	1
chr15:45658643	p.I293V	1
chr15:45661562	p.P183L	1
chr15:45658282	p.R290K	1
chr15:45658648	p.W149L	1
chr15:45661570	p.A286S	1
chr15:45658329	p.P146P	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 GATM 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 GATM

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


ABHD3,CCDC126,CD46,RHOV___CHP1,COL4A3BP,CPEB3,ENPP4, ETFDH,GATM,GPD1L,GPR160,MYO5C,PRR15L,SIDT1, SLC35A3,SNAP23,SPG11,SPPL2A,STAM2,SYPL1,TMEM30B	ATP1B1,SPRYD7,FBXO3,GATM,HSF2,KCNS3,LOC400027, MOB4,MOSPD1,NDFIP2,NDUFA5,PPP1CB,PPP1R2,RAB10, RAD1,RWDD4,TOB1,TSPYL1,UBQLN2,VAPA,VTA1

A4GNT,ACY3,ANXA10,BCAR4,BTBD16,CCER1,C9orf3, DRC7,CLTC,COX8C,CPS1,GABRP,GATA4,GATM, KY,LIPC,LOC100128239,PDZK1,PRKAR1A,SERPINA4,SLC16A2	AIG1,APOM,ASPA,BDH2,TMEM252,CYB5A,ESRRG, GATA5,GATM,GCNT4,HACL1,HOXC11,HOXC8,HOXC9, OAT,PEBP1,PEPD,PHEX,PHYHIPL,SAT2,TM4SF4

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 GATM

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
DB00129	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	approved; nutraceutical	L-Ornithine
DB00145	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	approved; nutraceutical	Glycine
DB02068	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	experimental	Delta-Amino Valeric Acid
DB02530	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	experimental	Gamma(Amino)-Butyric Acid
DB04185	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	experimental	Norvaline
DB04454	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	experimental	Alpha-Aminobutyric Acid
DB00125	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	approved; nutraceutical	L-Arginine
DB00515	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	approved	Cisplatin

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Cross referenced IDs for GATM

* 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