Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 AMPD1
Basic gene info.Gene symbolAMPD1
Gene nameadenosine monophosphate deaminase 1
SynonymsMAD|MADA|MMDD
CytomapUCSC genome browser: 1p13
Genomic locationchr1 :115215719-115238239
Type of geneprotein-coding
RefGenesNM_000036.2,
NM_001172626.1,
Ensembl idENSG00000116748
DescriptionAMP deaminase 1AMPDadenosine monophosphate deaminase 1 (isoform M)adenosine monophosphate deaminase-1 (muscle)myoadenylate deaminaseskeletal muscle AMPD
Modification date20141207
dbXrefs MIM : 102770
HGNC : HGNC
Ensembl : ENSG00000116748
HPRD : 00040
Vega : OTTHUMG00000011892
ProteinUniProt: P23109
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_AMPD1
BioGPS: 270
Gene Expression Atlas: ENSG00000116748
The Human Protein Atlas: ENSG00000116748
PathwayNCI Pathway Interaction Database: AMPD1
KEGG: AMPD1
REACTOME: AMPD1
ConsensusPathDB
Pathway Commons: AMPD1
MetabolismMetaCyc: AMPD1
HUMANCyc: AMPD1
RegulationEnsembl's Regulation: ENSG00000116748
miRBase: chr1 :115,215,719-115,238,239
TargetScan: NM_000036
cisRED: ENSG00000116748
ContextiHOP: AMPD1
cancer metabolism search in PubMed: AMPD1
UCL Cancer Institute: AMPD1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for AMPD1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: AMPD1
Familial Cancer Database: AMPD1
* 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/

check002.gifMetabolic Pathway Description
KEGG_PURINE_METABOLISM
REACTOME_METABOLISM_OF_NUCLEOTIDES
REACTOME_PURINE_METABOLISM

check002.gifOthers
OMIM 102770; gene.
615511; phenotype.
Orphanet 45; Adenosine monophosphate deaminase deficiency.
DiseaseKEGG Disease: AMPD1
MedGen: AMPD1 (Human Medical Genetics with Condition)
ClinVar: AMPD1
PhenotypeMGI: 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows AMPD1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BX647833AMPD116141115226831115238170FYTTD160837513197483395197511167

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy 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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check002.gifSNV 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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=112)
Stat. for Synonymous SNVs
(# total SNVs=21)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr1:115218614-115218614p.R467C4
chr1:115217379-115217379p.L598F4
chr1:115221019-115221019p.E343K3
chr1:115216304-115216304p.E681K3
chr1:115218219-115218219p.K537N3
chr1:115220030-115220030p.V444I3
chr1:115221096-115221096p.R317H3
chr1:115220031-115220031p.F443F3
chr1:115231345-115231345p.R18G3
chr1:115220970-115220970p.S359C3

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample151163 1  1 96421267116
# mutation151153 1  1 126421309122
nonsynonymous SNV141133 1    95321237119
synonymous SNV 1 2     1 311  72 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr1:115220124p.E372K,AMPD13
chr1:115221096p.R346H,AMPD13
chr1:115220970p.A441A,AMPD13
chr1:115221019p.S388C,AMPD13
chr1:115219982p.P662P,AMPD12
chr1:115226906p.P462S,AMPD12
chr1:115220031p.P223A,AMPD12
chr1:115216605p.K498N,AMPD12
chr1:115220063p.S183L,AMPD12
chr1:115226943p.E710K,AMPD12

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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

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
check002.gifCo-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

: Open all plots for all cancer types

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check002.gifInteracting 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 AMPD1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P23109; -.
ChemistryChEMBL CHEMBL2869; -.
Organism-specific databasesPharmGKB PA24776; -.
Organism-specific databasesCTD 270; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00173adenosine monophosphate deaminase 1approved; nutraceuticalAdenine
DB00640adenosine monophosphate deaminase 1approved; investigationalAdenosine
DB00158adenosine monophosphate deaminase 1approved; nutraceuticalFolic Acid
DB01076adenosine monophosphate deaminase 1approvedAtorvastatin
DB00439adenosine monophosphate deaminase 1withdrawnCerivastatin
DB01095adenosine monophosphate deaminase 1approvedFluvastatin
DB00175adenosine monophosphate deaminase 1approvedPravastatin
DB01098adenosine monophosphate deaminase 1approvedRosuvastatin
DB00641adenosine monophosphate deaminase 1approvedSimvastatin
DB00563adenosine monophosphate deaminase 1approvedMethotrexate


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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

: Open all cross reference information



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