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 GMPS
Basic gene info.Gene symbolGMPS
Gene nameguanine monphosphate synthase
Synonyms-
CytomapUCSC genome browser: 3q24
Genomic locationchr3 :155588324-155655520
Type of geneprotein-coding
RefGenesNM_003875.2,
Ensembl idENSG00000163655
DescriptionGMP synthaseGMP synthase [glutamine-hydrolyzing]GMP synthetaseMLL/GMPS fusion proteinglutamine amidotransferaseguanine monphosphate synthetaseguanosine 5'-monophosphate synthase
Modification date20141207
dbXrefs MIM : 600358
HGNC : HGNC
Ensembl : ENSG00000163655
HPRD : 10927
Vega : OTTHUMG00000158551
ProteinUniProt: P49915
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GMPS
BioGPS: 8833
Gene Expression Atlas: ENSG00000163655
The Human Protein Atlas: ENSG00000163655
PathwayNCI Pathway Interaction Database: GMPS
KEGG: GMPS
REACTOME: GMPS
ConsensusPathDB
Pathway Commons: GMPS
MetabolismMetaCyc: GMPS
HUMANCyc: GMPS
RegulationEnsembl's Regulation: ENSG00000163655
miRBase: chr3 :155,588,324-155,655,520
TargetScan: NM_003875
cisRED: ENSG00000163655
ContextiHOP: GMPS
cancer metabolism search in PubMed: GMPS
UCL Cancer Institute: GMPS
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for GMPS(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GMPS
Familial Cancer Database: GMPS
* 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
KEGG_DRUG_METABOLISM_OTHER_ENZYMES
REACTOME_METABOLISM_OF_NUCLEOTIDES
REACTOME_PURINE_METABOLISM

check002.gifOthers
OMIM 600358; gene.
Orphanet
DiseaseKEGG Disease: GMPS
MedGen: GMPS (Human Medical Genetics with Condition)
ClinVar: GMPS
PhenotypeMGI: GMPS (International Mouse Phenotyping Consortium)
PhenomicDB: GMPS

Mutations for GMPS
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryGMPSchr3155642643155642663GMPSchr3155642549155642569
ovaryGMPSchr3155649791155649811GMPSchr3155650012155650032
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GMPS related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AF297747MLL242611118352703118355690GMPS42515863155611305155633956
AF297748MLL117111118353172118355029GMPS1703533155611305155611488
AF297746MLL231211118352703118355029GMPS3116583155611305155621700
AF297749MLL128511118353172118355690GMPS2844673155611305155611488
AU132130CCDC14115122179912011179916447GMPS5116943155611305155611489

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 1      
GAIN (# sample)        1 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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=68)
Stat. for Synonymous SNVs
(# total SNVs=12)
Stat. for Deletions
(# total SNVs=2)
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
chr3:155628496-155628496p.S181F3
chr3:155628985-155628985p.V268A3
chr3:155652794-155652794p.R589H3
chr3:155652736-155652736p.E570*2
chr3:155655429-155655429p.R677Q2
chr3:155621691-155621691p.S122G2
chr3:155639983-155639983p.G442G2
chr3:155654194-155654194p.L625L2
chr3:155654195-155654195p.Q626*2
chr3:155652730-155652730p.V568I2

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample32116  3  1 1012  54110
# mutation32115  3  1 1112  64112
nonsynonymous SNV22113  3  1 9 1  63111
synonymous SNV1  2       211   1 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
chr3:155652794p.V268A3
chr3:155628985p.R589H3
chr3:155655458p.P687T2
chr3:155629063p.V50M1
chr3:155654202p.Q264R1
chr3:155611422p.I398I1
chr3:155633942p.P612P1
chr3:155624029p.R70C1
chr3:155649612p.V268M1
chr3:155632226p.G442D1

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 GMPS 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 GMPS

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

BUB1,CCNB2,DLGAP5,EXO1,GMPS,KIF20A,KIF23,
KIF4A,KPNA4,MCM6,MELK,MSH2,MSH6,NCAPG,
PLCH1,RFC4,SMC4,STIL,SUV39H2,TPX2,TTK
CCDC138,DSC2,FAM60A,GMPS,HDAC2,LARS,LRRC8D,
MSH2,MSH6,PAICS,PPAT,SEC23B,SET,SLC25A13,
SRP72,SRPK1,STIL,TDP1,TEX10,TMEM97,ZNF146

ACTL6A,CMSS1,CHEK1,ECT2,FBXO45,GMPS,KIAA1524,
MCM2,MRPL3,NAA50,NCAPH,POLQ,PRIM2,RFC4,
RSRC1,RUVBL1,SMC4,TOPBP1,TRA2B,TTK,UMPS
CCT3,CCT6A,CHEK1,CSE1L,FAM98A,GMPS,HSPD1,
IARS,IPO11,MCM6,NAA15,NOL10,PA2G4,PA2G4P4,
PAICS,RUVBL1,SERBP1,SET,STIP1,USP1,ZW10
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 GMPS
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryChEMBL CHEMBL5721; -.
Organism-specific databasesPharmGKB PA28763; -.
Organism-specific databasesCTD 8833; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00142guanine monphosphate synthaseapproved; nutraceuticalL-Glutamic Acid
DB02212guanine monphosphate synthaseexperimentalPyrophosphate 2-
DB04272guanine monphosphate synthaseexperimentalCitric Acid
DB00130guanine monphosphate synthaseapproved; nutraceutical; investigationalL-Glutamine


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Cross referenced IDs for GMPS
* 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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