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 APRT
Basic gene info.Gene symbolAPRT
Gene nameadenine phosphoribosyltransferase
SynonymsAMP|APRTD
CytomapUCSC genome browser: 16q24
Genomic locationchr16 :88875876-88878342
Type of geneprotein-coding
RefGenesNM_000485.2,
NM_001030018.1,
Ensembl idENSG00000198931
DescriptionAMP diphosphorylaseAMP pyrophosphorylasetransphosphoribosidase
Modification date20141219
dbXrefs MIM : 102600
HGNC : HGNC
Ensembl : ENSG00000198931
HPRD : 00029
Vega : OTTHUMG00000175454
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_APRT
BioGPS: 353
Gene Expression Atlas: ENSG00000198931
The Human Protein Atlas: ENSG00000198931
PathwayNCI Pathway Interaction Database: APRT
KEGG: APRT
REACTOME: APRT
ConsensusPathDB
Pathway Commons: APRT
MetabolismMetaCyc: APRT
HUMANCyc: APRT
RegulationEnsembl's Regulation: ENSG00000198931
miRBase: chr16 :88,875,876-88,878,342
TargetScan: NM_000485
cisRED: ENSG00000198931
ContextiHOP: APRT
cancer metabolism search in PubMed: APRT
UCL Cancer Institute: APRT
Assigned class in ccmGDBC

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

Mutations for APRT
* 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 APRT related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG475137APRT20106168887685288876939APRT103597168887588288876876
BQ222629TMEM185A1402X148682100148693035APRT402812168887647788878314

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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=8)
Stat. for Synonymous SNVs
(# total SNVs=6)
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
chr16:88876116-88876116p.Q178R2
chr16:88878307-88878307p.M1V2
chr16:88876845-88876845p.L103M1
chr16:88876887-88876887p.R89W1
chr16:88876134-88876134p.P172L1
chr16:88876893-88876893p.R87G1
chr16:88876189-88876189p.V154M1
chr16:88876924-88876924p.A76A1
chr16:88876190-88876190p.C153C1
chr16:88877971-88877971p.I58I1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1 12       1    23 2
# mutation1 12       1    23 2
nonsynonymous SNV           1    22  
synonymous SNV1 12             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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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
chr16:88877971p.C153C1
chr16:88876157p.V150V1
chr16:88878028p.T132A,APRT1
chr16:88876190p.L130L,APRT1
chr16:88878266p.Q121H,APRT1
chr16:88876199p.L103M,APRT1
chr16:88876484p.R89W,APRT1
chr16:88876490p.R87G,APRT1
chr16:88876515p.A76A,APRT1
chr16:88876845p.I58I,APRT1

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 APRT 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 APRT

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

APRT,AURKAIP1,UQCC3,C19orf60,CHMP1A,COPE,COX4I1,
CTU2,FAM96B,GADD45GIP1,KLHDC4,MRPL41,MVD,PDF,
RPL13,SPATA2L,SURF2,TMEM208,TRADD,TRAPPC2L,ZNF593
APRT,TEN1,CHID1,CNPY2,DDX49,EEF1D,EIF6,
EXOSC4,HMG20B,ITPA,LSM7,MRPS26,NHP2,NME2,
PES1,RPS15,RPUSD1,RUVBL2,SLC27A5,TIMM13,TRAPPC6A

APRT,UQCC3,C16orf13,COA4,COX4I1,CTU2,FAM195A,
FAM96B,MLST8,MRPS34,NDUFB10,NTHL1,NUBP2,NUTF2,
PPP4C,TEX264,THOC6,PAM16,TMEM208,TRAPPC2L,TUFM
AHCY,APRT,BID,TMEM258,DCTPP1,EXOSC5,KRTCAP3,
LSM7,MLST8,MRPS12,NME2,NR2C2AP,PFDN6,PHB2,
PHB,SF3B5,SNRPB,SYNGR2,TARBP2,THOC6,URM1
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 APRT
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
DB00173adenine phosphoribosyltransferaseapproved; nutraceuticalAdenine
DB01632adenine phosphoribosyltransferaseexperimentalAlpha-Phosphoribosylpyrophosphoric Acid
DB03506adenine phosphoribosyltransferaseexperimental9-Deazaadenine
DB04272adenine phosphoribosyltransferaseexperimentalCitric Acid
DB00640adenine phosphoribosyltransferaseapproved; investigationalAdenosine


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Cross referenced IDs for APRT
* 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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