Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 GNPDA2
Basic gene info.Gene symbolGNPDA2
Gene nameglucosamine-6-phosphate deaminase 2
SynonymsGNP2|SB52
CytomapUCSC genome browser: 4p12
Genomic locationchr4 :44704167-44728612
Type of geneprotein-coding
RefGenesNM_001270880.1,
NM_001270881.1,NM_138335.2,NR_073094.1,NR_073095.1,
Ensembl idENSG00000163281
DescriptionglcN6P deaminase 2glucosamine-6-phosphate isomerase 2glucosamine-6-phosphate isomerase SB52
Modification date20141207
dbXrefs MIM : 613222
HGNC : HGNC
Ensembl : ENSG00000163281
HPRD : 13594
Vega : OTTHUMG00000099415
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GNPDA2
BioGPS: 132789
Gene Expression Atlas: ENSG00000163281
The Human Protein Atlas: ENSG00000163281
PathwayNCI Pathway Interaction Database: GNPDA2
KEGG: GNPDA2
REACTOME: GNPDA2
ConsensusPathDB
Pathway Commons: GNPDA2
MetabolismMetaCyc: GNPDA2
HUMANCyc: GNPDA2
RegulationEnsembl's Regulation: ENSG00000163281
miRBase: chr4 :44,704,167-44,728,612
TargetScan: NM_001270880
cisRED: ENSG00000163281
ContextiHOP: GNPDA2
cancer metabolism search in PubMed: GNPDA2
UCL Cancer Institute: GNPDA2
Assigned class in ccmGDBC

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Phenotypic Information for GNPDA2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GNPDA2
Familial Cancer Database: GNPDA2
* 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: GNPDA2
MedGen: GNPDA2 (Human Medical Genetics with Condition)
ClinVar: GNPDA2
PhenotypeMGI: GNPDA2 (International Mouse Phenotyping Consortium)
PhenomicDB: GNPDA2

Mutations for GNPDA2
* 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 GNPDA2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=23)
Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr4:44709820-44709820p.D240N2
chr4:44713015-44713015p.T183T2
chr4:44709931-44709931p.I203V1
chr4:44713078-44713078p.L162L1
chr4:44705109-44705109p.D274N1
chr4:44720403-44720403p.K50R1
chr4:44712972-44712972p.E198*1
chr4:44713095-44713095p.T157A1
chr4:44705119-44705119p.F270F1
chr4:44720409-44720409p.C48F1

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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
# sample11 4       43   23 6
# mutation11 4       43   23 8
nonsynonymous SNV 1 3       32    3 8
synonymous SNV1  1       11   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
chr4:44709820p.D206N,GNPDA22
chr4:44713010p.T123A,GNPDA21
chr4:44720409p.G241V,GNPDA21
chr4:44705105p.K92K,GNPDA21
chr4:44713031p.F236F,GNPDA21
chr4:44724108p.K92R,GNPDA21
chr4:44705119p.V218V,GNPDA21
chr4:44713035p.G75W,GNPDA21
chr4:44724174p.D208H,GNPDA21
chr4:44709782p.D64N,GNPDA21

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 GNPDA2 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 GNPDA2

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

BOD1L1,C5orf24,CDK17,CSNK1G3,DMXL1,FBXL5,GNPDA2,
GUF1,HAUS3,CFAP97,MBLAC2,PDS5A,PLA2G12A,PREPL,
SCAMP1,SEPSECS,SLC30A9,TRIM23,UBE2K,WDR19,ZNF721
ANKRD13C,C16orf52,CAPN7,CGGBP1,FAM8A1,FBXO28,GNPDA2,
LANCL1,LRRC40,MIER1,MTMR6,NAPG,NSL1,PCNP,
RAB5A,SEPT10,TM9SF3,TRAPPC6B,TROVE2,UFM1,VAMP4

BBS10,BMI1,C5orf24,CCDC91,CREG1,DUSP19,FAM200B,
GABPA,GLIPR1L2,GNPDA2,KBTBD3,LIAS,PACRGL,PIGY,
RAB28,TBC1D19,TIPRL,TMEM128,TMEM55A,UBE2K,VAMP4
ARPP19,ATL2,C9orf3,CETN2,CFL2,CLIC4,DNAJC24,
DPT,MICU3,EID1,ZC2HC1A,COX20,GNG11,GNPDA2,
HIAT1,SCHIP1,SEPT7,TCEAL1,TCEAL7,ZNF25,ZNF781
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 GNPDA2


There's no related Drug.
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Cross referenced IDs for GNPDA2
* 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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