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 GNPDA1
Basic gene info.Gene symbolGNPDA1
Gene nameglucosamine-6-phosphate deaminase 1
SynonymsGNP1|GNPDA|GNPI|GPI|HLN
CytomapUCSC genome browser: 5q21
Genomic locationchr5 :141380233-141392620
Type of geneprotein-coding
RefGenesNM_005471.4,
Ensembl idENSG00000113552
DescriptionGNPDA 1glcN6P deaminase 1glucosamine-6-phosphate isomerase 1oscillin
Modification date20141207
dbXrefs MIM : 601798
HGNC : HGNC
Ensembl : ENSG00000113552
HPRD : 09048
Vega : OTTHUMG00000129657
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GNPDA1
BioGPS: 10007
Gene Expression Atlas: ENSG00000113552
The Human Protein Atlas: ENSG00000113552
PathwayNCI Pathway Interaction Database: GNPDA1
KEGG: GNPDA1
REACTOME: GNPDA1
ConsensusPathDB
Pathway Commons: GNPDA1
MetabolismMetaCyc: GNPDA1
HUMANCyc: GNPDA1
RegulationEnsembl's Regulation: ENSG00000113552
miRBase: chr5 :141,380,233-141,392,620
TargetScan: NM_005471
cisRED: ENSG00000113552
ContextiHOP: GNPDA1
cancer metabolism search in PubMed: GNPDA1
UCL Cancer Institute: GNPDA1
Assigned class in ccmGDBC

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Phenotypic Information for GNPDA1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GNPDA1
Familial Cancer Database: GNPDA1
* 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_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GNPDA1
MedGen: GNPDA1 (Human Medical Genetics with Condition)
ClinVar: GNPDA1
PhenotypeMGI: GNPDA1 (International Mouse Phenotyping Consortium)
PhenomicDB: GNPDA1

Mutations for GNPDA1
* 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 GNPDA1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
N45950GNPDA11795141380562141380640GNPDA1753635141380253141380539
BU619601GNPDA1132015141380236141382699GNPDA11965795141381388141382729
BU618872GNPDA1132005141380236141382699GNPDA11955785141381388141382729
AA383455GNPDA113985141380559141380644PPP2R2B951155146299111146299131
W00428GNPDA12825141380560141380640GNPDA1783775141380241141380539
BE162856KLHL10187206174000132040001339GNPDA11943295141380648141380783

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=11)
Stat. for Synonymous SNVs
(# total SNVs=3)
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
chr5:141391532-141391532p.R23R3
chr5:141385882-141385882p.R79Q2
chr5:141384531-141384531p.T187M2
chr5:141391505-141391505p.E32D2
chr5:141391553-141391553p.A16A1
chr5:141381655-141381655p.Y270C1
chr5:141385781-141385781p.D113N1
chr5:141391557-141391557p.W15L1
chr5:141381656-141381656p.Y270H1
chr5:141385836-141385838p.F94delF1

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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   2  1 1  2    13 3
# mutation   2  1 1  2    13 2
nonsynonymous SNV   2  1 1  2     3 2
synonymous SNV                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
chr5:141391505p.E32D2
chr5:141381655p.R158C1
chr5:141391485p.T157T1
chr5:141381656p.G139C1
chr5:141382753p.G136A1
chr5:141384619p.C118Y1
chr5:141384620p.D113N1
chr5:141384676p.R79Q1
chr5:141385711p.K67N1
chr5:141385765p.L39H1

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 GNPDA1 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 GNPDA1

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

ATP6V1C1,CCDC43,CDC23,FAM114A2,GEMIN5,GNPDA1,H2AFY,
HARS2,HSPA9,LARS,MRPS27,NDFIP1,PAIP2,PPP2CA,
RAD17,RBM22,RNF14,SNX24,TMEM67,VDAC1,ZMAT2
AIF1,ARPC5,ARRB2,C1orf162,C1orf85,C1QB,CD33,
CHST13,FCER1G,FUCA1,GNPDA1,GSTO1,LGALS9,LST1,
NAGA,NLRC4,NPC2,RNASE6,SLC7A7,STMN1,TNFAIP8L2

ABCF2,AHCY,ATP5E,ATP6V1F,COPRS,C20orf24,MALSU1,
CDK5,EIF2S2,GNPDA1,HDAC3,MRPS23,NIT2,PDRG1,
PDZD11,PSMA7,PSMB3,RAE1,ROMO1,TP53RK,UQCC1
ALDH1A1,ATP6V1B2,CISD1,CUTC,CYB5A,DKFZp779M0652,FTL,
GATM,GNPDA1,LMO4,NINJ1,PFN2,RWDD2A,SCPEP1,
SIRT2,SIRT4,SNX2,STOML1,VKORC1,ZBTB14,ZNF16
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 GNPDA1
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
DB02379glucosamine-6-phosphate deaminase 1experimentalBeta-D-Glucose
DB02445glucosamine-6-phosphate deaminase 1experimental2-Deoxy-2-Amino Glucitol-6-Phosphate
DB03951glucosamine-6-phosphate deaminase 1experimental16g


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Cross referenced IDs for GNPDA1
* 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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