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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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TissGeneSummary

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TissGeneExp

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TissGene-miRNA

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TissGeneMut: TissGeneSNV, TissGeneCNV, and TissGeneFusions

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TissGeneNet

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TissGeneProg

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TissGeneClin: TissGeneDrug and TissGeneDisease

TissGeneSummary for GAMT
check button Gene summary
Basic gene informationGene symbolGAMT
Gene nameguanidinoacetate N-methyltransferase
SynonymsCCDS2|HEL-S-20|PIG2|TP53I2
CytomapUCSC genome browser: 19p13.3
Type of geneprotein-coding
RefGenesNM_000156.5,
NM_138924.2,
Descriptionepididymis secretory protein Li 20
Modification date20141219
dbXrefs MIM : 601240
HGNC : HGNC
Ensembl : ENSG00000130005
HPRD : 03142
Vega : OTTHUMG00000180095
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GAMT
BioGPS: 2593
PathwayNCI Pathway Interaction Database: GAMT
KEGG: GAMT
REACTOME: GAMT
Pathway Commons: GAMT
ContextiHOP: GAMT
ligand binding site mutation search in PubMed: GAMT
UCL Cancer Institute: GAMT
Assigned class in TissGDB*C
Included tissue-specific gene expression resourcesTiGER,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)Liver
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)LIHC
Reference showing the relevant tissue of GAMT
Description by TissGene annotations
* 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.

check button Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO termPubMed ID
GO:0006601creatine biosynthetic process8651275
GO:0006601creatine biosynthetic process8651275


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TissGeneExp for GAMT

check button 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 exp


check button 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 isoform exp


check button 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.
normal gene exp


check button 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)
DEG exp

- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05)
Cancer typeMean(exp) in tumorMean(exp) in matched normalLog2FCP-val.FDR
STAD-1.6947885620.337636438-2.0324252.31E-088.81E-07
LUSC0.10945096-0.9907215891.1001725492.06E-075.60E-07
HNSC-0.1012620361.419630987-1.5208930239.13E-065.24E-05
KICH-0.3331146871.611373313-1.9444882.81E-081.39E-07
ESCA-1.9038485060.639333313-2.5431818180.0002970.006809567
BLCA-1.2156930030.46931226-1.6850052630.0003350.002968287
COAD-2.748101303-1.561708995-1.1863923088.79E-050.000326422


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TissGene-miRNA for GAMT

check button 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 typemiRNA idmiRNA accessionP-val.Coeff.# samples


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TissGeneMut for GAMT
TissGeneSNV for GAMT

check button 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.
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check button 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)
SNV distribution

- nsSNVs sorted by frequency.
AAchangeCancer type# samples
p.P227LESCA2
p.E191DHNSC1
p.W174CBRCA1
p.V95IUCEC1
p.A156TUCEC1
p.E118KSKCM1
p.Y223CCOAD1
p.G208RSKCM1
p.S173FSKCM1
p.R158CHNSC1
p.L218IESCA1
p.R100WUCEC1
p.K153ECOAD1
p.G175ESKCM1
p.P217LGBM1
p.R158HCOAD1
p.M228ISKCM1


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TissGeneCNV for GAMT

check button 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)
CNV


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TissGeneFusions for GAMT

check button Fusion genes including TissGene
(ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01)
DatabaseSrcCancer typeSampleFusion geneORF5'-gene BP3'-gene BP


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TissGeneNet for GAMT

check button 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)
GAMT, S100A9, POT1, FOS, ELANE, CSNK2B, TERF2IP (tumor)GAMT, S100A9, POT1, FOS, ELANE, CSNK2B, TERF2IP (normal)
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COAD (tumor)COAD (normal)
GAMT, S100A9, POT1, FOS, ELANE, CSNK2B, TERF2IP (tumor)GAMT, S100A9, POT1, FOS, ELANE, CSNK2B, TERF2IP (normal)
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HNSC (tumor)HNSC (normal)
GAMT, S100A9, POT1, FOS, ELANE, CSNK2B, TERF2IP (tumor)GAMT, S100A9, POT1, FOS, ELANE, CSNK2B, TERF2IP (normal)
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KICH (tumor)KICH (normal)
GAMT, S100A9, POT1, FOS, ELANE, CSNK2B, TERF2IP (tumor)GAMT, S100A9, POT1, FOS, ELANE, CSNK2B, TERF2IP (normal)
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KIRC (tumor)KIRC (normal)
GAMT, S100A9, POT1, FOS, ELANE, CSNK2B, TERF2IP (tumor)GAMT, S100A9, POT1, FOS, ELANE, CSNK2B, TERF2IP (normal)
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KIRP (tumor)KIRP (normal)
GAMT, S100A9, POT1, FOS, ELANE, CSNK2B, TERF2IP (tumor)GAMT, S100A9, POT1, FOS, ELANE, CSNK2B, TERF2IP (normal)
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LIHC (tumor)LIHC (normal)
GAMT, S100A9, POT1, FOS, ELANE, CSNK2B, TERF2IP (tumor)GAMT, S100A9, POT1, FOS, ELANE, CSNK2B, TERF2IP (normal)
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LUAD (tumor)LUAD (normal)
GAMT, S100A9, POT1, FOS, ELANE, CSNK2B, TERF2IP (tumor)GAMT, S100A9, POT1, FOS, ELANE, CSNK2B, TERF2IP (normal)
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LUSC (tumor)LUSC (normal)
GAMT, S100A9, POT1, FOS, ELANE, CSNK2B, TERF2IP (tumor)GAMT, S100A9, POT1, FOS, ELANE, CSNK2B, TERF2IP (normal)
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PRAD (tumor)PRAD (normal)
GAMT, S100A9, POT1, FOS, ELANE, CSNK2B, TERF2IP (tumor)GAMT, S100A9, POT1, FOS, ELANE, CSNK2B, TERF2IP (normal)
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STAD (tumor)STAD (normal)
GAMT, S100A9, POT1, FOS, ELANE, CSNK2B, TERF2IP (tumor)GAMT, S100A9, POT1, FOS, ELANE, CSNK2B, TERF2IP (normal)
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THCA (tumor)THCA (normal)
GAMT, S100A9, POT1, FOS, ELANE, CSNK2B, TERF2IP (tumor)GAMT, S100A9, POT1, FOS, ELANE, CSNK2B, TERF2IP (normal)
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TissGeneProg for GAMT

check button 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.
survival 1

check button 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.
survival 2

check button 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.
survival 3

check button 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.
survival 4

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TissGeneClin for GAMT
TissGeneDrug for GAMT

check button Drug information targeting TissGene
(DrugBank Version 5.0.6, 2017-04-01)
DrugBank IDDrug nameDrug activityDrug typeDrug status
DB00148CreatineProduct ofSmall moleculeApproved|Nutraceutical


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TissGeneDisease for GAMT

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0574080Guanidinoacetate methyltransferase deficiency5BeFree,CLINVAR,CTD_human,MGD,ORPHANET,UNIPROT
umls:C1845862Creatine deficiency, X-linked2BeFree
umls:C0002514Amino Acid Metabolism, Inborn Errors1CTD_human
umls:C0036572Seizures1CTD_human
umls:C0080178Spina Bifida1GAD
umls:C0948008Ischemic stroke1BeFree
umls:C3272363Ischemic Cerebrovascular Accident1BeFree
umls:C3714756Intellectual Disability1CTD_human