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 GMPR2
Basic gene info.Gene symbolGMPR2
Gene nameguanosine monophosphate reductase 2
Synonyms-
CytomapUCSC genome browser: 14q12
Genomic locationchr14 :24701647-24708447
Type of geneprotein-coding
RefGenesNM_001002000.2,
NM_001002001.2,NM_001002002.2,NM_001283021.1,NM_001283022.1,
NM_001283023.1,NM_016576.4,NR_104265.1,
Ensembl idENSG00000100938
DescriptionGMP reductase 2guanosine 5'-monophosphate oxidoreductase 2guanosine monophosphate reductase isolog
Modification date20141207
dbXrefs MIM : 610781
HGNC : HGNC
Ensembl : ENSG00000100938
HPRD : 13590
Vega : OTTHUMG00000171912
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GMPR2
BioGPS: 51292
Gene Expression Atlas: ENSG00000100938
The Human Protein Atlas: ENSG00000100938
PathwayNCI Pathway Interaction Database: GMPR2
KEGG: GMPR2
REACTOME: GMPR2
ConsensusPathDB
Pathway Commons: GMPR2
MetabolismMetaCyc: GMPR2
HUMANCyc: GMPR2
RegulationEnsembl's Regulation: ENSG00000100938
miRBase: chr14 :24,701,647-24,708,447
TargetScan: NM_001002000
cisRED: ENSG00000100938
ContextiHOP: GMPR2
cancer metabolism search in PubMed: GMPR2
UCL Cancer Institute: GMPR2
Assigned class in ccmGDBC

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Phenotypic Information for GMPR2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GMPR2
Familial Cancer Database: GMPR2
* 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: GMPR2
MedGen: GMPR2 (Human Medical Genetics with Condition)
ClinVar: GMPR2
PhenotypeMGI: GMPR2 (International Mouse Phenotyping Consortium)
PhenomicDB: GMPR2

Mutations for GMPR2
* 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 GMPR2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AK075025GMPR211165142470166624707667STOML21161206493509989335101490
BF916399JUN112315924792359248045GMPR2116288142470818424708356

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample        1        
GAIN (# sample)        1        
LOSS (# sample)                 
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=13)
Stat. for Synonymous SNVs
(# total SNVs=9)
Stat. for Deletions
(# total SNVs=1)
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
chr14:24706339-24706339p.I176M2
chr14:24707977-24707977p.A347V2
chr14:24702539-24702539p.R27Q2
chr14:24704989-24704989p.W85S1
chr14:24707478-24707478p.G242R1
chr14:24707913-24707913p.E326*1
chr14:24705248-24705248p.V123M1
chr14:24707479-24707479p.G242D1
chr14:24707939-24707939p.I334I1
chr14:24705334-24705334p.Q151Q1

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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
# sample 1 5  1    2 2  32 5
# mutation 1 4  1    2 2  32 6
nonsynonymous SNV 1 2  1      2  21 3
synonymous SNV   2       2    11 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
chr14:24702528p.T41T,GMPR22
chr14:24705248p.Q169Q,GMPR21
chr14:24707806p.I194I,GMPR21
chr14:24705324p.K231N,GMPR21
chr14:24707820p.D245Y,GMPR21
chr14:24705334p.F250F,GMPR21
chr14:24707945p.G260R,GMPR21
chr14:24706339p.L263L,GMPR21
chr14:24707966p.F361V,GMPR21
chr14:24706542p.P14S,GMPR21

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 GMPR2 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 GMPR2

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

ACOT4,AP1G2,DHRS4-AS1,DCAF11,EAPP,GMPR2,HOMEZ,
KHNYN,KLHDC2,LRP10,MDP1,NEDD8,OXA1L,PIGH,
PSME1,RNF31,THTPA,TINF2,TM9SF1,TOX4,TTC8
ARMCX6,C10orf35,C11orf52,C14orf93,DALRD3,DGCR2,DNAL4,
ELMO3,FBL,GMPR2,ING4,MED29,MRFAP1L1,MRPL49,
NR2C2AP,PRKCZ,RAB25,RPL3,SPINT2,STK16,TTLL1

ALKBH1,APEX1,DNAAF2,C14orf119,DTD2,C14orf166,CGRRF1,
CHMP4A,CNIH1,DAD1,EAPP,GMPR2,HAUS4,ISCA2,
KIAA0391,MDP1,NEDD8,RPS29,SNX6,TMEM55B,ZNF410
BLOC1S1,TEN1,LINC00324,RPP25L,CCNDBP1,CHMP5,DERA,
EAPP,GABARAP,GMPR2,HINFP,HOXB7,MAT2B,OAZ1,
LAMTOR2,SAT1,TMEM219,TMEM59,UBAC2,VPS28,ZNF706
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 GMPR2


There's no related Drug.
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Cross referenced IDs for GMPR2
* 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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