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 NAGK
Basic gene info.Gene symbolNAGK
Gene nameN-acetylglucosamine kinase
SynonymsGNK|HSA242910
CytomapUCSC genome browser: 2p13.3
Genomic locationchr2 :71295407-71305998
Type of geneprotein-coding
RefGenesNM_017567.4,
Ensembl idENSG00000124357
DescriptionN-acetyl-D-glucosamine kinaseglcNAc kinase
Modification date20141207
dbXrefs MIM : 606828
HGNC : HGNC
Ensembl : ENSG00000124357
HPRD : 08441
Vega : OTTHUMG00000153239
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NAGK
BioGPS: 55577
Gene Expression Atlas: ENSG00000124357
The Human Protein Atlas: ENSG00000124357
PathwayNCI Pathway Interaction Database: NAGK
KEGG: NAGK
REACTOME: NAGK
ConsensusPathDB
Pathway Commons: NAGK
MetabolismMetaCyc: NAGK
HUMANCyc: NAGK
RegulationEnsembl's Regulation: ENSG00000124357
miRBase: chr2 :71,295,407-71,305,998
TargetScan: NM_017567
cisRED: ENSG00000124357
ContextiHOP: NAGK
cancer metabolism search in PubMed: NAGK
UCL Cancer Institute: NAGK
Assigned class in ccmGDBC

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

Mutations for NAGK
* 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 NAGK related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ334962PFN112131748491374849349NAGK20726927130576471305826
AW748767NAGK138727130029971300374NAGK8535727130005571300326

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=23)
Stat. for Synonymous SNVs
(# total SNVs=16)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr2:71297643-71297643p.R14Q3
chr2:71304726-71304726p.C268C3
chr2:71297682-71297682p.L27R2
chr2:71297695-71297695p.D31D2
chr2:71304751-71304751p.E277Q2
chr2:71305438-71305438p.?2
chr2:71302769-71302769p.E222K2
chr2:71303793-71303793p.G243S2
chr2:71298852-71298852p.G84W1
chr2:71305540-71305540p.L313V1

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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
# sample21 8    2  34   13 5
# mutation21 8    2  34   13 6
nonsynonymous SNV11 5    2  22   11 2
synonymous SNV1  3       12    2 4
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
chr2:71302769p.E268K2
chr2:71299880p.V66I1
chr2:71303790p.D226G1
chr2:71297660p.L79L1
chr2:71300618p.I227I1
chr2:71303799p.I95N1
chr2:71297699p.C263C1
chr2:71300632p.S122S1
chr2:71304726p.A129V1
chr2:71297902p.Y279H1

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 NAGK 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 NAGK

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

AP2S1,APOE,AURKAIP1,BAX,C19orf60,C1orf122,PRADC1,
CCDC124,CCM2,EDF1,FASTK,IRF3,MGAT1,MRPL53,
NAGK,NDUFS7,SIRT6,TMSB10,TRADD,TWF2,VAMP5
ARPC4,C17orf62,C19orf10,MFSD12,CAPG,CCDC137,CNPY3,
CORO7,CRELD2,CYBA,GBAP1,GRN,LRPAP1,NAGK,
REEP4,RNASET2,SHKBP1,SIPA1,STX4,TMED9,TRADD

ABI3,ADAP2,AIF1,CD300A,CYTH4,DOK2,HAVCR2,
HCST,IFFO1,LAIR1,LSP1,LST1,MGAT1,MYO1F,
NAGK,PIK3R6,PLEKHO2,PPM1M,SPI1,TNFAIP8L2,TYROBP
AIF1,APOBEC3G,C19orf38,C1orf162,CD300C,CD40,CYBB,
DOK2,FCER1G,GIMAP4,GIMAP5,HCST,KYNU,LST1,
NAGK,NCF2,OSCAR,PDCD1LG2,SPI1,TNFAIP8L2,TYROBP
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 NAGK
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
DB00141N-acetylglucosamine kinaseapproved; nutraceuticalN-Acetyl-D-glucosamine


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Cross referenced IDs for NAGK
* 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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