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 NDST3
Basic gene info.Gene symbolNDST3
Gene nameN-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3
SynonymsHSST3
CytomapUCSC genome browser: 4q26
Genomic locationchr4 :118955499-119179789
Type of geneprotein-coding
RefGenesNM_004784.2,
Ensembl idENSG00000164100
DescriptionGlcNAc N-deacetylase/ N-sulfotransferase 3N-HSST 3N-heparan sulfate sulfotransferase 3NDST-3bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3glucosaminyl N-deacetylase/N-sulfotransferase 3hNDST-3
Modification date20141207
dbXrefs MIM : 603950
HGNC : HGNC
Ensembl : ENSG00000164100
Vega : OTTHUMG00000132959
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NDST3
BioGPS: 9348
Gene Expression Atlas: ENSG00000164100
The Human Protein Atlas: ENSG00000164100
PathwayNCI Pathway Interaction Database: NDST3
KEGG: NDST3
REACTOME: NDST3
ConsensusPathDB
Pathway Commons: NDST3
MetabolismMetaCyc: NDST3
HUMANCyc: NDST3
RegulationEnsembl's Regulation: ENSG00000164100
miRBase: chr4 :118,955,499-119,179,789
TargetScan: NM_004784
cisRED: ENSG00000164100
ContextiHOP: NDST3
cancer metabolism search in PubMed: NDST3
UCL Cancer Institute: NDST3
Assigned class in ccmGDBC

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Phenotypic Information for NDST3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NDST3
Familial Cancer Database: NDST3
* 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: NDST3
MedGen: NDST3 (Human Medical Genetics with Condition)
ClinVar: NDST3
PhenotypeMGI: NDST3 (International Mouse Phenotyping Consortium)
PhenomicDB: NDST3

Mutations for NDST3
* 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
breastNDST3chr4119006912119006912chr2073233627323362
breastNDST3chr4119006912119006912NDST3chr4119012493119012493
ovaryNDST3chr4119055224119055244NDST3chr4119051288119051308
pancreasNDST3chr4119147667119147687chr4178214553178214573
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 NDST3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AV697913RPS615129691937625319376507NDST32873104118999891118999914

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      1   
GAIN (# sample) 1           1   
LOSS (# sample)      1          
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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=87)
Stat. for Synonymous SNVs
(# total SNVs=24)
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
chr4:118975673-118975673p.R203H3
chr4:119059310-119059310p.W442C3
chr4:118976014-118976014p.E317K3
chr4:118975397-118975397p.A111V3
chr4:118975856-118975856p.H264R3
chr4:119161842-119161842p.P761L3
chr4:119154278-119154278p.R644M2
chr4:119036052-119036052p.P387P2
chr4:119158200-119158200p.?2
chr4:119064735-119064735p.L479F2

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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
# sample231182 5 4  125 112314110
# mutation231162 6 4  125 112515115
nonsynonymous SNV211141 3 1  84 1 2010114
synonymous SNV 2 21 3 3  41  155 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
chr4:118975856p.H264R3
chr4:119059263p.V427I3
chr4:119148127p.R203H2
chr4:119154231p.S425S2
chr4:119059259p.P241T2
chr4:118975786p.S245Y2
chr4:118975799p.P603P2
chr4:118975673p.P628P2
chr4:119064745p.L772Q1
chr4:119163220p.A189T1

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 NDST3 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 NDST3

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

AFF2,C17orf51,CHRNA3,GABRG2,KCNK10,LOC100133545,MET,
MMP26,NDST3,NTS,P2RX6,PCSK1,PDGFRA,PRMT8,
PTPRN,PTX3,RASSF9,SLC10A4,TMEFF2,TNMD,VGF
ACTBL2,CA13,CBLN4,CHN1,CLDN1,DEFB131,FAM133A,
FAM3C,KCNK2,LXN,MAPK1IP1L,NDST3,NDST4,NUS1,
OR6Y1,RGS2,SLC26A2,SOCS5,STXBP3,TBK1,UBLCP1

CH25H,COL9A1,CORIN,DKK3,F2R,F2RL2,FAT4,
FIBIN,FOXF1,GLI1,GPR1,IP6K3,ITGA11,KLHL13,
NDST3,PCDH18,PDGFC,PDZD2,SDC2,TNFSF11,WNT2
ADORA2B,ALDH3A1,ARL15,CNTN4,EFNB2,EPB41L5,BRINP2,
HAS3,LANCL3,LOC723809,MIER3,NDST3,NFE2L2,NPHS2,
NRG1,RPL10L,SLC20A1,UGDH,UGT1A10,UGT1A8,ZNF800
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 NDST3


There's no related Drug.
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Cross referenced IDs for NDST3
* 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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