Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 AMPD2
Basic gene info.Gene symbolAMPD2
Gene nameadenosine monophosphate deaminase 2
SynonymsPCH9|SPG63
CytomapUCSC genome browser: 1p13.3
Genomic locationchr1 :110168048-110174677
Type of geneprotein-coding
RefGenesNM_001257360.1,
NM_001257361.1,NM_004037.7,NM_139156.3,NM_203404.1,
Ensembl idENSG00000116337
DescriptionAMP deaminase 2AMPDadenosine monophosphate deaminase 2 (isoform L)
Modification date20141207
dbXrefs MIM : 102771
HGNC : HGNC
Ensembl : ENSG00000116337
HPRD : 11808
Vega : OTTHUMG00000011649
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_AMPD2
BioGPS: 271
Gene Expression Atlas: ENSG00000116337
The Human Protein Atlas: ENSG00000116337
PathwayNCI Pathway Interaction Database: AMPD2
KEGG: AMPD2
REACTOME: AMPD2
ConsensusPathDB
Pathway Commons: AMPD2
MetabolismMetaCyc: AMPD2
HUMANCyc: AMPD2
RegulationEnsembl's Regulation: ENSG00000116337
miRBase: chr1 :110,168,048-110,174,677
TargetScan: NM_001257360
cisRED: ENSG00000116337
ContextiHOP: AMPD2
cancer metabolism search in PubMed: AMPD2
UCL Cancer Institute: AMPD2
Assigned class in ccmGDBC

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Phenotypic Information for AMPD2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: AMPD2
Familial Cancer Database: AMPD2
* 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: AMPD2
MedGen: AMPD2 (Human Medical Genetics with Condition)
ClinVar: AMPD2
PhenotypeMGI: AMPD2 (International Mouse Phenotyping Consortium)
PhenomicDB: AMPD2

Mutations for AMPD2
* 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 AMPD2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BC030217NEAT11249116519027765190525AMPD223916911110172058110174677
BI021213PCIF162253204456613744566328AMPD22533951110174531110174673

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=1

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=6)
Stat. for Synonymous SNVs
(# total SNVs=0)
There's no s-snv.
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr1:110170826-110170826p.T374M1
chr1:110170900-110170900p.?1
chr1:110173662-110173662p.R762H1
chr1:110168351-110168351p.S70N1
chr1:110168805-110168805p.R99Q1
chr1:110168974-110168974p.D125E1
chr1:110169394-110169394p.A166V1

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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
# sample11 172 3 1  6141110816
# mutation21 182 3 1  6141110917
nonsynonymous SNV11 141 2 1  514113816
synonymous SNV1  41 1    1    71 1
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
chr1:110173662p.R724H,AMPD23
chr1:110172893p.D87E,AMPD22
chr1:110170826p.A528E,AMPD22
chr1:110168974p.R88Q,AMPD22
chr1:110172028p.T336K,AMPD22
chr1:110168976p.I609I,AMPD22
chr1:110163659p.L8L,AMPD22
chr1:110170727p.S303W,AMPD22
chr1:110171292p.D87G,AMPD21
chr1:110168351p.R313L,AMPD21

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 AMPD2 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 AMPD2

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

AMPD2,ARHGAP22,ATAD3A,ATXN7L2,CCDC102A,CTU2,E2F4,
FHL3,KIFC3,MAP7D1,PLEKHM2,PLOD3,POLR2F,PPAN,
PSRC1,RNF166,RRP1,SLC39A13,TMEM39B,WDR46,ZDHHC8
AMPD2,C17orf70,CACNB3,CNOT3,CXXC1,EHMT2,FBXL19,
GPSM1,KRBA1,LLGL1,PITPNM1,POLD1,SEPT9,SLC12A9,
SMO,SNAPC4,SRC,TCF3,TRAF7,TRIM28,TSC22D4

ALX3,AMIGO1,AMPD2,ATXN7L2,CYB561D1,DHX38,DPH2,
DPH3P1,STRIP1,MROH1,INTS1,IPO13,JRK,MAFG,
MCM3AP,NPHP4,PRDM15,SMG5,USP24,ZBTB40,ZCCHC14
AMPD2,ANAPC2,ANO8,C17orf70,CHPF,CPSF1,CUL9,
DENND4B,LOC150197,MAN2A2,PCSK4,PDE4DIP,POLM,PPP1R3E,
SARM1,TCF3,TOP3B,TUBGCP6,WDR24,XPC,ZFP41
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 AMPD2
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 2approved; nutraceuticalAdenine
DB00640adenosine monophosphate deaminase 2approved; investigationalAdenosine


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Cross referenced IDs for AMPD2
* 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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