TissGDB

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	TissGeneSummary
	TissGeneExp
	TissGene-miRNA
	TissGeneMut: TissGeneSNV, TissGeneCNV, and TissGeneFusions
	TissGeneNet
	TissGeneProg
	TissGeneClin: TissGeneDrug and TissGeneDisease

TissGeneSummary for GATM

Gene summary

Basic gene information	Gene symbol	GATM
	Gene name	glycine amidinotransferase (L-arginine:glycine amidinotransferase)
	Synonyms	AGAT\|AT\|CCDS3
	Cytomap	UCSC genome browser: 15q21.1
	Type of gene	protein-coding
	RefGenes	NM_001482.2,
	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
Pathway	NCI Pathway Interaction Database: GATM
	KEGG: GATM
	REACTOME: GATM
	Pathway Commons: GATM
Context	iHOP: GATM
	ligand binding site mutation search in PubMed: GATM
	UCL Cancer Institute: GATM
Assigned class in TissGDB*	C
Included tissue-specific gene expression resources	TiGER,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)	KidneyLiverPancreas
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)	KIRC,KIRP,KICHLIHCPAAD
Reference showing the relevant tissue of GATM
Description by TissGene annotations	Fused withTSGene

* Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

GO ID	GO term	PubMed ID
GO:0006601	creatine biosynthetic process	9218780
GO:0006601	creatine biosynthetic process	9218780

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TissGeneExp for GATM

Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)

Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01)

Gene expressions across normal tissues of GTEx data
(GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct)
- Here, we shows the matched tissue types only among our 28 cancer types.

Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)

- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05)

Cancer type	Mean(exp) in tumor	Mean(exp) in matched normal	Log2FC	P-val.	FDR
KIRC	3.059034308	4.380923197	-1.321888889	3.82E-05	8.47E-05
KICH	-0.711371359	3.854820641	-4.566192	1.10E-10	8.42E-10
HNSC	-2.154142242	0.235469386	-2.389611628	2.02E-09	2.97E-08
PRAD	-2.191782359	-0.621151589	-1.570630769	6.94E-18	2.11E-15
LIHC	4.883190641	6.348794641	-1.465604	2.01E-08	1.66E-07
THCA	-0.479771765	1.155079082	-1.634850847	1.17E-12	1.02E-11
KIRP	2.976755141	4.935617641	-1.9588625	0.00103	0.002829975
COAD	-1.799053512	-0.615784282	-1.183269231	0.00018	0.000614299

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TissGene-miRNA for GATM

Significantly anti-correlated miRNAs of TissGene across 28 cancer types
(Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016)
(TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21)
(TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16)
(Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25))

Cancer type	miRNA id	miRNA accession	P-val.	Coeff.	# samples
UCEC	hsa-let-7a-5p	MIMAT0000062	0.00018	-0.27	194
UCS	hsa-miR-30b-5p	MIMAT0000420	0.029	-0.29	56

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TissGeneMut for GATM

TissGeneSNV for GATM

nsSNV counts per each loci.
Different colors of circles represent different cancer types. Circle size denotes number of samples.
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)
* Click on the image to enlarge it in a new window.

Somatic nucleotide variants of TissGene across 28 cancer types
(X-axis: cancer type and Y-axis: % of mutated samples)
The numbers in parentheses are numbers of samples with mutation (nsSNVs).
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)

- nsSNVs sorted by frequency.

AAchange	Cancer type	# samples
p.I259F	BRCA	1
p.R187L	LUAD	1
p.R26Q	SKCM	1
p.W335*	SKCM	1
p.R282C	UCEC	1
p.E279K	BLCA	1
p.R414H	SKCM	1
p.R414C	HNSC	1
p.V245A	OV	1
p.G314R	SKCM	1
p.I293V	HNSC	1
p.G402E	BLCA	1
p.N132T	UCEC	1
p.P340S	LUAD	1
p.G262V	BRCA	1
p.P183L	SKCM	1
p.R47G	KIRC	1
p.P105L	SKCM	1
p.H406R	MESO	1
p.P90L	HNSC	1
p.D63A	LIHC	1
p.T389S	UCEC	1
p.A286S	BRCA	1
p.H119N	UCEC	1
p.I388V	LUAD	1
p.D63N	SKCM	1
p.E181K	SKCM	1
p.E126V	BRCA	1
p.Y196H	LUAD	1
p.R206L	LUAD	1
p.P378S	STAD	1
p.R194Q	HNSC	1
p.R290K	LUSC	1
p.F36L	GBM	1
p.R187C	STAD	1
p.D226G	LIHC	1
p.R34Q	BLCA	1
p.R189H	COAD	1
p.Q241R	STAD	1
p.S295F	SKCM	1
p.L151S	LIHC	1
p.D298G	GBM	1
p.F253L	LIHC	1
p.W149L	LUAD	1
p.L75X	KIRP	1
p.D298Y	UCEC	1
p.T247A	UCEC	1

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TissGeneCNV for GATM

Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples)
(TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16)

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TissGeneFusions for GATM

Fusion genes including TissGene
(ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01)

Database	Src	Cancer type	Sample	Fusion gene	ORF	5'-gene BP	3'-gene BP
Chimerdb3.0	ChiTaRs	NA	BF933512	GATM-DDX3X		chr15:45656463	chrX:41197147
Chimerdb3.0	ChiTaRs	NA	AW861199	WSB1-GATM		chr17:25630602	chr15:45657895
Chimerdb3.0	ChiTaRs	NA	BF946024	GATM-TSEN2		chr15:45654108	chr3:12560544

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TissGeneNet for GATM

Co-expressed gene networks based on protein-protein interaction data (CePIN)
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(PINA2 ppi data)

BRCA (tumor)	BRCA (normal)
GATM, CYP2E1 (tumor)	GATM, CYP2E1 (normal)

COAD (tumor)	COAD (normal)
GATM, CYP2E1 (tumor)	GATM, CYP2E1 (normal)

HNSC (tumor)	HNSC (normal)
GATM, CYP2E1 (tumor)	GATM, CYP2E1 (normal)

KICH (tumor)	KICH (normal)
GATM, CYP2E1 (tumor)	GATM, CYP2E1 (normal)

KIRC (tumor)	KIRC (normal)
GATM, CYP2E1 (tumor)	GATM, CYP2E1 (normal)

KIRP (tumor)	KIRP (normal)
GATM, CYP2E1 (tumor)	GATM, CYP2E1 (normal)

LIHC (tumor)	LIHC (normal)
GATM, CYP2E1 (tumor)	GATM, CYP2E1 (normal)

LUAD (tumor)	LUAD (normal)
GATM, CYP2E1 (tumor)	GATM, CYP2E1 (normal)

LUSC (tumor)	LUSC (normal)
GATM, CYP2E1 (tumor)	GATM, CYP2E1 (normal)

PRAD (tumor)	PRAD (normal)
GATM, CYP2E1 (tumor)	GATM, CYP2E1 (normal)

STAD (tumor)	STAD (normal)
GATM, CYP2E1 (tumor)	GATM, CYP2E1 (normal)

THCA (tumor)	THCA (normal)
GATM, CYP2E1 (tumor)	GATM, CYP2E1 (normal)

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TissGeneProg for GATM

Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)
* Click on the image to enlarge it in a new window.

Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)
* Click on the image enlarge it in a new window.

Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)
* Click on the image enlarge it in a new window.

Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)
* Click on the image enlarge it in a new window.

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TissGeneClin for GATM

TissGeneDrug for GATM

Drug information targeting TissGene
(DrugBank Version 5.0.6, 2017-04-01)

DrugBank ID	Drug name	Drug activity	Drug type	Drug status
DB00145	Glycine		Small molecule	Approved\|Nutraceutical\|Vet_approved

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TissGeneDisease for GATM

Disease information associated with TissGene
(DisGeNet, 2016-06-01)

Disease ID	Disease name	# pubmeds	Source
umls:C2675179	Arginine:Glycine Amidinotransferase Deficiency	3	BeFree,CLINVAR,CTD_human,ORPHANET,UNIPROT
umls:C0026848	Myopathy	2	BeFree
umls:C0007134	Renal Cell Carcinoma	1	BeFree
umls:C0008312	Primary biliary cirrhosis	1	BeFree
umls:C0018801	Heart failure	1	BeFree,CTD_human
umls:C0018802	Congestive heart failure	1	BeFree
umls:C0022658	Kidney Diseases	1	CTD_human
umls:C0024667	Animal Mammary Neoplasms	1	CTD_human
umls:C0024668	Mammary Neoplasms, Experimental	1	CTD_human
umls:C0027540	Necrosis	1	CTD_human
umls:C0151744	Myocardial Ischemia	1	CTD_human
umls:C0376358	Malignant neoplasm of prostate	1	BeFree
umls:C0574080	Guanidinoacetate methyltransferase deficiency	1	BeFree
umls:C0600139	Prostate carcinoma	1	BeFree
umls:C1845862	Creatine deficiency, X-linked	1	BeFree
umls:C1853195	Prostate Cancer, Hereditary, 7	1	BeFree
umls:C2609414	Acute kidney injury	1	RGD