Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 PRPS1
Basic gene info.Gene symbolPRPS1
Gene namephosphoribosyl pyrophosphate synthetase 1
SynonymsARTS|CMTX5|DFN2|DFNX1|PPRibP|PRS-I|PRSI
CytomapUCSC genome browser: Xq22.3
Genomic locationchrX :106871653-106894256
Type of geneprotein-coding
RefGenesNM_001204402.1,
NM_002764.3,
Ensembl idENSG00000147224
DescriptiondJ1070B1.2 (phosphoribosyl pyrophosphate synthetase 1)deafness 2, perceptive, congenitaldeafness, X-linked 2, perceptive, congenitalphosphoribosyl pyrophosphate synthase Iribose-phosphate diphosphokinase 1ribose-phosphate pyrophosphokinase 1
Modification date20141219
dbXrefs MIM : 311850
HGNC : HGNC
Ensembl : ENSG00000147224
HPRD : 02413
Vega : OTTHUMG00000022167
ProteinUniProt: P60891
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PRPS1
BioGPS: 5631
Gene Expression Atlas: ENSG00000147224
The Human Protein Atlas: ENSG00000147224
PathwayNCI Pathway Interaction Database: PRPS1
KEGG: PRPS1
REACTOME: PRPS1
ConsensusPathDB
Pathway Commons: PRPS1
MetabolismMetaCyc: PRPS1
HUMANCyc: PRPS1
RegulationEnsembl's Regulation: ENSG00000147224
miRBase: chrX :106,871,653-106,894,256
TargetScan: NM_001204402
cisRED: ENSG00000147224
ContextiHOP: PRPS1
cancer metabolism search in PubMed: PRPS1
UCL Cancer Institute: PRPS1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

Top
Phenotypic Information for PRPS1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PRPS1
Familial Cancer Database: PRPS1
* 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_CARBOHYDRATES

check002.gifOthers
OMIM 300661; phenotype.
301835; phenotype.
304500; phenotype.
311070; phenotype.
311850; gene.
Orphanet 1187; Lethal ataxia with deafness and optic atrophy.
3222; Phosphoribosylpyrophosphate synthetase superactivity.
90625; X-linked non-syndromic sensorineural deafness type DFN.
99014; X-linked Charcot-Marie-Tooth disease type 5.
DiseaseKEGG Disease: PRPS1
MedGen: PRPS1 (Human Medical Genetics with Condition)
ClinVar: PRPS1
PhenotypeMGI: PRPS1 (International Mouse Phenotyping Consortium)
PhenomicDB: PRPS1

Mutations for PRPS1
* 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 PRPS1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BM553232PRPS121151X106871759106871888TMEM91137188194188993741889988
DA717960PRPS1154X106871745106871798PRKCB54573162384760724104212

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

Top
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.

Top
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=6

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=29)
Stat. for Synonymous SNVs
(# total SNVs=7)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

Top
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
chr23:106888484-106888484p.D203G3
chr23:106888532-106888532p.V219A3
chr23:106882595-106882595p.D65Y3
chr23:106888483-106888483p.D203H2
chr23:106890928-106890928p.F266S2
chr23:106882703-106882703p.D101Y1
chr23:106890870-106890870p.I247F1
chr23:106884133-106884133p.S103N1
chr23:106890894-106890894p.G255C1
chr23:106885605-106885605p.D139H1

Top
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
# sample 1 10  3 3  43   2 14
# mutation 1 6  3 3  44   2 15
nonsynonymous SNV   5  3 3  32   1 13
synonymous SNV 1 1       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])

Top
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
chrX:106888484p.D203G3
chrX:106888531p.V15M,PRPS12
chrX:106888532p.V15A,PRPS12
chrX:106882680p.S117S1
chrX:106888430p.G51C,PRPS11
chrX:106893241p.D139H1
chrX:106882686p.E63E,PRPS11
chrX:106888476p.D143D1
chrX:106882703p.L108L,PRPS11
chrX:106884133p.W154L1

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 PRPS1 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]

Top
Gene Expression for PRPS1

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

ATP5L2,DPP3,FLJ44635,GH1,HCN2,KCNJ2,MAP3K3,
MRPL11,PC,PELI3,PRPS1L1,RCE1,RNFT1,RPL31P11,
RPS6KB1,SMARCD2,STRADA,SUCNR1,SYT12,TCAM1P,ZDHHC24
ATP11AUN,C7orf71,CGB2,DEFB125,GH2,GNG8,HDGFL1,
HELT,IAPP,IFNA5,KRTAP13-2,LHX9,OR10J5,OR2M3,
PRDM7,PRPS1L1,PSG8,SLC17A3,SLC6A19,SNORA59B,TAS2R13

ANXA2P3,CSNK1A1L,EIF3IP1,FLJ44635,HSP90B3P,LOC100132831,LOC341056,
LOC442308,LOC649330,LOC723972,NME2P1,POTEM,PA2G4P4,PIN1P1,
POTEF,PRPS1L1,RPL19P12,RPL31P11,SBF1P1,UBE2NL,WBP11P1
ACSL3,ACTL8,ATP12A,BACE2,TDRP,CLINT1,GAPDHS,
IL19,KIR2DL1,LPCAT2,NEK6,PLA2G2A,POTEC,PRPS1L1,
PRSS22,RAB27B,SLC10A7,SLC16A14,SLC38A5,TMEM173,ZNF486
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for PRPS1


There's no related Drug.
Top
Cross referenced IDs for PRPS1
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas