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 GNS
Basic gene info.Gene symbolGNS
Gene nameglucosamine (N-acetyl)-6-sulfatase
SynonymsG6S
CytomapUCSC genome browser: 12q14
Genomic locationchr12 :65107221-65153226
Type of geneprotein-coding
RefGenesNM_002076.3,
Ensembl idENSG00000135677
DescriptionN-acetylglucosamine-6-sulfataseglucosamine-6-sulfatase
Modification date20141207
dbXrefs MIM : 607664
HGNC : HGNC
Ensembl : ENSG00000135677
HPRD : 09637
Vega : OTTHUMG00000168819
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GNS
BioGPS: 2799
Gene Expression Atlas: ENSG00000135677
The Human Protein Atlas: ENSG00000135677
PathwayNCI Pathway Interaction Database: GNS
KEGG: GNS
REACTOME: GNS
ConsensusPathDB
Pathway Commons: GNS
MetabolismMetaCyc: GNS
HUMANCyc: GNS
RegulationEnsembl's Regulation: ENSG00000135677
miRBase: chr12 :65,107,221-65,153,226
TargetScan: NM_002076
cisRED: ENSG00000135677
ContextiHOP: GNS
cancer metabolism search in PubMed: GNS
UCL Cancer Institute: GNS
Assigned class in ccmGDBC

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

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

Mutations for GNS
* 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
There's no inter-chromosomal structural variation.
- 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
ovaryGNSchr126512706165127081chr126462567264625692
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 GNS related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CR741239NPHP3-ACAD1111883132400417132400604GNS184494126510872765109037
AI701812AKAP9118679171945791719642GNS186416126510742165107650
N40382OPTN195101316099713164435GNS94439126510869865109037
BQ434418CAND118312126769610167696395GNS311529126511538365116895
DB469756ZNF691137314331225443316740GNS368453126510883565108920
CA449339GNS18453126510722965107664NCAM2448732212255898422559273
BE708454GNS1339126513803665138375ESRP133149689571880995718977

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 # sample11      1 3  11  
GAIN (# sample)11      1 3  11  
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=36)
Stat. for Synonymous SNVs
(# total SNVs=8)
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
chr12:65134422-65134422p.S280Y2
chr12:65137006-65137006p.S236L2
chr12:65146499-65146499p.M77I2
chr12:65115486-65115486p.?2
chr12:65130842-65130842p.D347V2
chr12:65137060-65137060p.Y218C2
chr12:65134405-65134405p.D286N1
chr12:65138659-65138659p.T185I1
chr12:65113896-65113896p.D496H1
chr12:65116868-65116868p.R409Q1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample3216  2 1  12   24 8
# mutation3218  2 1  12   24 8
nonsynonymous SNV2 17  1 1   1   23 5
synonymous SNV12 1  1    11    1 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
chr12:65134422p.S280Y2
chr12:65138647p.N189S1
chr12:65113896p.D441N1
chr12:65130795p.G161R1
chr12:65139483p.S430F1
chr12:65113900p.M77I1
chr12:65130829p.K549N1
chr12:65146499p.V412V1
chr12:65110533p.D380D1
chr12:65113930p.G75E1

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 GNS 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 GNS

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

AFF4,APC,APOOL,C12orf66,CANX,CCNT1,CHM,
FNIP1,GNS,LEMD3,LMBRD2,MON2,PLBD2,RAPGEF6,
RASSF3,SERINC3,SERINC5,SLC25A46,TBK1,TTC37,UEVLD
ANGPT1,ARHGAP21,ASAH1,ASPH,BHMT2,CHRDL1,DENND5A,
ECM2,EPB41L2,GLP2R,GNG2,GNS,ITGB1,ITSN1,
KLHL5,LAMA4,RHOQ,SEPT11,SORBS1,STS,ZDHHC3

C3AR1,CSF1,CSF1R,CTSB,GIT2,GNS,LAPTM5,
LRRC25,MAFB,MNDA,MYO5A,NRP1,PDCD1LG2,PLBD2,
PLXNC1,PSAP,PTAFR,RAB8B,SSH1,TLR1,TSHZ2
ABCD1,AHCYL1,APC,ATRN,CREB3L2,EXOC6B,GNS,
LONP2,MAOB,NBAS,NUCB1,OSR2,PI4K2A,PLOD1,
SEC31A,SIRPA,SLC9A6,SMC3,TMEM25,TPP1,UBE2R2
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 GNS


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