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 AMPD3
Basic gene info.Gene symbolAMPD3
Gene nameadenosine monophosphate deaminase 3
Synonyms-
CytomapUCSC genome browser: 11p15
Genomic locationchr11 :10476665-10529126
Type of geneprotein-coding
RefGenesNM_000480.2,
NM_001025389.1,NM_001025390.1,NM_001172430.1,NM_001172431.1,
Ensembl idENSG00000133805
DescriptionAMP aminohydrolaseAMP deaminase 3adenosine monophosphate deaminase (isoform E)erythrocyte AMP deaminaseerythrocyte type AMP deaminaseerythrocyte-specific AMP deaminasemyoadenylate deaminase
Modification date20141207
dbXrefs MIM : 102772
HGNC : HGNC
Ensembl : ENSG00000133805
HPRD : 00041
Vega : OTTHUMG00000165682
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_AMPD3
BioGPS: 272
Gene Expression Atlas: ENSG00000133805
The Human Protein Atlas: ENSG00000133805
PathwayNCI Pathway Interaction Database: AMPD3
KEGG: AMPD3
REACTOME: AMPD3
ConsensusPathDB
Pathway Commons: AMPD3
MetabolismMetaCyc: AMPD3
HUMANCyc: AMPD3
RegulationEnsembl's Regulation: ENSG00000133805
miRBase: chr11 :10,476,665-10,529,126
TargetScan: NM_000480
cisRED: ENSG00000133805
ContextiHOP: AMPD3
cancer metabolism search in PubMed: AMPD3
UCL Cancer Institute: AMPD3
Assigned class in ccmGDBC

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Phenotypic Information for AMPD3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: AMPD3
Familial Cancer Database: AMPD3
* 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
Orphanet
DiseaseKEGG Disease: AMPD3
MedGen: AMPD3 (Human Medical Genetics with Condition)
ClinVar: AMPD3
PhenotypeMGI: AMPD3 (International Mouse Phenotyping Consortium)
PhenomicDB: AMPD3

Mutations for AMPD3
* 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 AMPD3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI027290CLEC18A1183167015241470152597AMPD3179406111051803910518266
AW882230AMPD314236111049583210496054PTMS2323011268798126879881
CD109332AMPD31114111047194710472060IER3103370620432972043564
BF915326AMPD319251111049480510495037MAN1B12505419139981514139983346

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=54)
Stat. for Synonymous SNVs
(# total SNVs=13)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=1)

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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
chr11:10483070-10483070p.P11S2
chr11:10500095-10500095p.R91W2
chr11:10527270-10527270p.L724M2
chr11:10503622-10503622p.D156N2
chr11:10508849-10508849p.E302K2
chr11:10527315-10527315p.R739*2
chr11:10515037-10515037p.G370C2
chr11:10527398-10527398p.M766I2
chr11:10472592-10472592p.?1
chr11:10527417-10527417p.A773S1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample41181 1 3  4711 191516
# mutation411101 1 3  4811 211617
nonsynonymous SNV31 81 1 3  161  161415
synonymous SNV1 12       32 1 52 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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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
chr11:10527398p.M598I,AMPD32
chr11:10506536p.E134K,AMPD32
chr11:10508849p.T94T,AMPD32
chr11:10483070p.A597D,AMPD31
chr11:10508889p.P108S,AMPD31
chr11:10521693p.H101Y,AMPD31
chr11:10500089p.P236L,AMPD31
chr11:10515084p.N347S,AMPD31
chr11:10527272p.P113L,AMPD31
chr11:10503755p.A239V,AMPD31

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 AMPD3 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 AMPD3

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

AMPD3,BTK,CD4,CD53,CXorf21,CYBB,DOCK2,
EVI2B,FYB,GPR65,LAPTM5,LCP2,MARCH1,MPEG1,
NCKAP1L,PIK3CG,PLEK,PTAFR,PTPRC,SNX20,TFEC
AMPD3,ATP8A1,CAB39,CACNA2D1,CD38,COL19A1,DENND4B,
FAM78A,GPA33,HTR7,LACTB,LOC728989,LRRC66,MBP,
OSBPL11,P2RX5,P2RX6,RCSD1,SEMA4D,SHD,SMYD2

ALOX5AP,AMPD3,ARHGAP31,THEMIS2,CSF1R,ETS1,GPR176,
HCK,ITGAM,ITGAX,MYO5A,NLRP3,PHLDB1,PLXNC1,
SIGLEC5,SIRPB2,TLR1,TLR2,WISP1,ZEB2,ZNF469
AMPD3,ANKZF1,ANO7,CACNA2D2,COL2A1,INSM1,KIAA1147,
KIAA1324,MAP3K1,MCF2L,MUTYH,NEIL1,NEK8,NKX2-2,
PGBD2,PTPRN2,RAP1GAP,SIAH2,SLC38A11,SYTL1,ZNF253
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 AMPD3
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00173adenosine monophosphate deaminase 3approved; nutraceuticalAdenine
DB00640adenosine monophosphate deaminase 3approved; investigationalAdenosine


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Cross referenced IDs for AMPD3
* 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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