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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for AMPD1 |
Basic gene info. | Gene symbol | AMPD1 |
Gene name | adenosine monophosphate deaminase 1 | |
Synonyms | MAD|MADA|MMDD | |
Cytomap | UCSC genome browser: 1p13 | |
Genomic location | chr1 :115215719-115238239 | |
Type of gene | protein-coding | |
RefGenes | NM_000036.2, NM_001172626.1, | |
Ensembl id | ENSG00000116748 | |
Description | AMP deaminase 1AMPDadenosine monophosphate deaminase 1 (isoform M)adenosine monophosphate deaminase-1 (muscle)myoadenylate deaminaseskeletal muscle AMPD | |
Modification date | 20141207 | |
dbXrefs | MIM : 102770 | |
HGNC : HGNC | ||
Ensembl : ENSG00000116748 | ||
HPRD : 00040 | ||
Vega : OTTHUMG00000011892 | ||
Protein | UniProt: P23109 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_AMPD1 | |
BioGPS: 270 | ||
Gene Expression Atlas: ENSG00000116748 | ||
The Human Protein Atlas: ENSG00000116748 | ||
Pathway | NCI Pathway Interaction Database: AMPD1 | |
KEGG: AMPD1 | ||
REACTOME: AMPD1 | ||
ConsensusPathDB | ||
Pathway Commons: AMPD1 | ||
Metabolism | MetaCyc: AMPD1 | |
HUMANCyc: AMPD1 | ||
Regulation | Ensembl's Regulation: ENSG00000116748 | |
miRBase: chr1 :115,215,719-115,238,239 | ||
TargetScan: NM_000036 | ||
cisRED: ENSG00000116748 | ||
Context | iHOP: AMPD1 | |
cancer metabolism search in PubMed: AMPD1 | ||
UCL Cancer Institute: AMPD1 | ||
Assigned class in ccmGDB | B - This gene belongs to cancer gene. |
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Phenotypic Information for AMPD1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: AMPD1 |
Familial Cancer Database: AMPD1 |
* This gene is included in those cancer gene databases. |
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_PURINE_METABOLISM REACTOME_METABOLISM_OF_NUCLEOTIDES REACTOME_PURINE_METABOLISM |
Others | |
OMIM | 102770; gene. 615511; phenotype. |
Orphanet | 45; Adenosine monophosphate deaminase deficiency. |
Disease | KEGG Disease: AMPD1 |
MedGen: AMPD1 (Human Medical Genetics with Condition) | |
ClinVar: AMPD1 | |
Phenotype | MGI: AMPD1 (International Mouse Phenotyping Consortium) |
PhenomicDB: AMPD1 |
Mutations for AMPD1 |
* 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 AMPD1 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 |
BX647833 | AMPD1 | 1 | 614 | 1 | 115226831 | 115238170 | FYTTD1 | 608 | 3751 | 3 | 197483395 | 197511167 |
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=112) | (# total SNVs=21) |
(# total SNVs=2) | (# total SNVs=0) |
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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 |
chr1:115218614-115218614 | p.R467C | 4 |
chr1:115217379-115217379 | p.L598F | 4 |
chr1:115218219-115218219 | p.K537N | 3 |
chr1:115220030-115220030 | p.V444I | 3 |
chr1:115221096-115221096 | p.R317H | 3 |
chr1:115220031-115220031 | p.F443F | 3 |
chr1:115231345-115231345 | p.R18G | 3 |
chr1:115220970-115220970 | p.S359C | 3 |
chr1:115223060-115223060 | p.R196Q | 3 |
chr1:115220069-115220069 | p.R431C | 3 |
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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 | 5 | 1 | 16 | 3 |   | 1 |   |   | 1 |   | 9 | 6 | 4 | 2 | 1 | 26 | 7 | 1 | 16 |
# mutation | 1 | 5 | 1 | 15 | 3 |   | 1 |   |   | 1 |   | 12 | 6 | 4 | 2 | 1 | 30 | 9 | 1 | 22 |
nonsynonymous SNV | 1 | 4 | 1 | 13 | 3 |   | 1 |   |   |   |   | 9 | 5 | 3 | 2 | 1 | 23 | 7 | 1 | 19 |
synonymous SNV |   | 1 |   | 2 |   |   |   |   |   | 1 |   | 3 | 1 | 1 |   |   | 7 | 2 |   | 3 |
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 |
chr1:115220970 | p.A441A,AMPD1 | 3 |
chr1:115221019 | p.S388C,AMPD1 | 3 |
chr1:115220124 | p.E372K,AMPD1 | 3 |
chr1:115221096 | p.R346H,AMPD1 | 3 |
chr1:115216605 | p.K498N,AMPD1 | 2 |
chr1:115220063 | p.S183L,AMPD1 | 2 |
chr1:115226943 | p.E710K,AMPD1 | 2 |
chr1:115218606 | p.P489S,AMPD1 | 2 |
chr1:115223067 | p.R171W,AMPD1 | 2 |
chr1:115216304 | p.F472L,AMPD1 | 2 |
Other DBs for Point Mutations |
Copy Number for AMPD1 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 AMPD1 |
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 |
AMPD1,APOBEC2,ATP1B4,C10orf71,MIR1-1HG,CACNA1S,CKM, CSRP3,FBXO40,MYH1,MYH6,MYH7,MYL1,MYL2, MYLPF,NEB,NRAP,PYGM,TMOD4,TTN,UNC45B | AMPD1,ANKRD23,APOBEC2,ASB11,ATP1B4,CASQ1,CHRNG, FSD2,KLHL41,KLHL40,KCNA7,LRRC39,MB,MYBPC2, MYH13,MYOG,SMTNL1,TMOD4,TNNI1,TNNI2,TTN | ||||
ADAM6,AMICA1,AMPD1,CD1D,CPNE5,CYSLTR1,DERL3, ENPP6,FCRL5,FLJ40330,GFRA2,IRF4,KCNA3,KCNN3, LAX1,MEI1,MZB1,PIM2,PNOC,SCARA5,TNFRSF17 | ADAM28,AHRR,AMPD1,BMP6,LACC1,SLX4IP,CD163L1, FAM46C,FLJ40330,GPR15,ITGA4,KREMEN1,KRTAP4-1,LAMC3, PDK1,RUNX2,SALL1,SCUBE1,SMOC1,TNFRSF17,TXNDC5 |
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 AMPD1 |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Chemistry | BindingDB | P23109; -. |
Chemistry | ChEMBL | CHEMBL2869; -. |
Organism-specific databases | PharmGKB | PA24776; -. |
Organism-specific databases | CTD | 270; -. |
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 |
DB00173 | adenosine monophosphate deaminase 1 | approved; nutraceutical | Adenine | ||
DB00640 | adenosine monophosphate deaminase 1 | approved; investigational | Adenosine | ||
DB00158 | adenosine monophosphate deaminase 1 | approved; nutraceutical | Folic Acid | ||
DB01076 | adenosine monophosphate deaminase 1 | approved | Atorvastatin | ||
DB00439 | adenosine monophosphate deaminase 1 | withdrawn | Cerivastatin | ||
DB01095 | adenosine monophosphate deaminase 1 | approved | Fluvastatin | ||
DB00175 | adenosine monophosphate deaminase 1 | approved | Pravastatin | ||
DB01098 | adenosine monophosphate deaminase 1 | approved | Rosuvastatin | ||
DB00641 | adenosine monophosphate deaminase 1 | approved | Simvastatin | ||
DB00563 | adenosine monophosphate deaminase 1 | approved | Methotrexate |
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Cross referenced IDs for AMPD1 |
* 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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