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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for GAMT |
Basic gene info. | Gene symbol | GAMT |
Gene name | guanidinoacetate N-methyltransferase | |
Synonyms | CCDS2|HEL-S-20|PIG2|TP53I2 | |
Cytomap | UCSC genome browser: 19p13.3 | |
Genomic location | chr19 :1397024-1401569 | |
Type of gene | protein-coding | |
RefGenes | NM_000156.5, NM_138924.2, | |
Ensembl id | ENSG00000130005 | |
Description | epididymis secretory protein Li 20 | |
Modification date | 20141219 | |
dbXrefs | MIM : 601240 | |
HGNC : HGNC | ||
Ensembl : ENSG00000130005 | ||
HPRD : 03142 | ||
Vega : OTTHUMG00000180095 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_GAMT | |
BioGPS: 2593 | ||
Gene Expression Atlas: ENSG00000130005 | ||
The Human Protein Atlas: ENSG00000130005 | ||
Pathway | NCI Pathway Interaction Database: GAMT | |
KEGG: GAMT | ||
REACTOME: GAMT | ||
ConsensusPathDB | ||
Pathway Commons: GAMT | ||
Metabolism | MetaCyc: GAMT | |
HUMANCyc: GAMT | ||
Regulation | Ensembl's Regulation: ENSG00000130005 | |
miRBase: chr19 :1,397,024-1,401,569 | ||
TargetScan: NM_000156 | ||
cisRED: ENSG00000130005 | ||
Context | iHOP: GAMT | |
cancer metabolism search in PubMed: GAMT | ||
UCL Cancer Institute: GAMT | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for GAMT(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: GAMT |
Familial Cancer Database: GAMT |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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: GAMT |
MedGen: GAMT (Human Medical Genetics with Condition) | |
ClinVar: GAMT | |
Phenotype | MGI: GAMT (International Mouse Phenotyping Consortium) |
PhenomicDB: GAMT |
Mutations for GAMT |
* 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 GAMT 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 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=17) | (# total SNVs=4) |
(# total SNVs=1) | (# 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 |
chr19:1399836-1399836 | p.V95I | 4 |
chr19:1397456-1397456 | p.E205* | 3 |
chr19:1399129-1399129 | p.K153E | 1 |
chr19:1398910-1398910 | p.? | 1 |
chr19:1399170-1399170 | p.L139fs*22 | 1 |
chr19:1398924-1398924 | p.I187I | 1 |
chr19:1399181-1399181 | p.D135E | 1 |
chr19:1398961-1398961 | p.G175E | 1 |
chr19:1399536-1399536 | p.D126D | 1 |
chr19:1398963-1398963 | p.W174C | 1 |
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SNV Counts per Each Loci in TCGA data |
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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 |   |   |   | 1 |   |   |   |   |   |   |   | 3 |   |   | 4 |
# mutation |   | 1 |   | 4 | 1 |   |   |   | 1 |   |   |   |   |   |   |   | 3 |   |   | 5 |
nonsynonymous SNV |   | 1 |   | 3 | 1 |   |   |   |   |   |   |   |   |   |   |   | 3 |   |   | 3 |
synonymous SNV |   |   |   | 1 |   |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   | 2 |
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 |
chr19:1398963 | p.R158H,GAMT | 1 |
chr19:1398967 | p.A156T,GAMT | 1 |
chr19:1399012 | p.H155H,GAMT | 1 |
chr19:1399019 | p.D126D,GAMT | 1 |
chr19:1399020 | p.R100W,GAMT | 1 |
chr19:1397385 | p.V95I,GAMT | 1 |
chr19:1399536 | p.V78V,GAMT | 1 |
chr19:1397401 | p.M228I | 1 |
chr19:1399821 | p.Y223C | 1 |
chr19:1397419 | p.P217L | 1 |
Other DBs for Point Mutations |
Copy Number for GAMT 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 GAMT |
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. |
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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 |
BLOC1S1,C19orf24,C19orf25,CHCHD5,MZT2B,FAM173A,FAM195A, GAMT,GPX4,HEXIM2,NAA38,MRPL54,NDUFA2,NDUFS7, NME3,NPDC1,PHPT1,TEX264,TMEM219,UQCR11,ZNF688 | ADPRHL1,PERM1,CHRNA10,CHRNB1,CLCN1,DYRK1B,EEF1A2, FEM1A,FHL3,GAMT,GOT1,JSRP1,MYL6B,OBSCN, PFKM,RTN2,SEMA6C,SHISA4,SRPK3,TPM2,WDR62 | ||||
ARSB,ASTN2,COL22A1,DIRAS1,EFNB3,FAM133A,FGL1, FOLH1,FOXE1,GABBR2,GAMT,MYO3B,NLGN2,OR10C1, PAGE1,PNMA6A,SLC7A2,SNCA,TLL2,TPH1,TUB | ARL3,CDPF1,CCDC106,CNRIP1,CRTAP,CUEDC2,CYB5R1, FBXO27,GAMT,GYPC,LOC158572,MAGED2,MAGEH1,OAZ2, SMARCD3,TCEA2,TCTN1,TMEM121,TNFSF12,ZFP82,ZNF667 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for GAMT |
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 |
DB00148 | guanidinoacetate N-methyltransferase | approved; nutraceutical | Creatine | ||
DB00536 | guanidinoacetate N-methyltransferase | approved | Guanidine | ||
DB01752 | guanidinoacetate N-methyltransferase | experimental | S-Adenosyl-L-Homocysteine | ||
DB02751 | guanidinoacetate N-methyltransferase | experimental | N-[Amino(Imino)Methyl]Glycine | ||
DB00145 | guanidinoacetate N-methyltransferase | approved; nutraceutical | Glycine | ||
DB00125 | guanidinoacetate N-methyltransferase | approved; nutraceutical | L-Arginine |
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Cross referenced IDs for GAMT |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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