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 NDST2
Basic gene info.Gene symbolNDST2
Gene nameN-deacetylase/N-sulfotransferase (heparan glucosaminyl) 2
SynonymsHSST2|NST2
CytomapUCSC genome browser: 10q22
Genomic locationchr10 :75561668-75571589
Type of geneprotein-coding
RefGenesNM_003635.3,
Ensembl idENSG00000166507
DescriptionN-HSST 2N-heparan sulfate sulfotransferase 2NDST-2bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 2glucosaminyl N-deacetylase/N-sulfotransferase 2
Modification date20141207
dbXrefs MIM : 603268
HGNC : HGNC
Ensembl : ENSG00000166507
HPRD : 04465
Vega : OTTHUMG00000018489
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NDST2
BioGPS: 8509
Gene Expression Atlas: ENSG00000166507
The Human Protein Atlas: ENSG00000166507
PathwayNCI Pathway Interaction Database: NDST2
KEGG: NDST2
REACTOME: NDST2
ConsensusPathDB
Pathway Commons: NDST2
MetabolismMetaCyc: NDST2
HUMANCyc: NDST2
RegulationEnsembl's Regulation: ENSG00000166507
miRBase: chr10 :75,561,668-75,571,589
TargetScan: NM_003635
cisRED: ENSG00000166507
ContextiHOP: NDST2
cancer metabolism search in PubMed: NDST2
UCL Cancer Institute: NDST2
Assigned class in ccmGDBC

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Phenotypic Information for NDST2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NDST2
Familial Cancer Database: NDST2
* 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: NDST2
MedGen: NDST2 (Human Medical Genetics with Condition)
ClinVar: NDST2
PhenotypeMGI: NDST2 (International Mouse Phenotyping Consortium)
PhenomicDB: NDST2

Mutations for NDST2
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
haematopoietic_and_lymphoid_tissueNDST2chr107556574275565742chr88214565682145656
haematopoietic_and_lymphoid_tissueNDST2chr107556576275565762chr10104145320104145320
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 NDST2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
T05579NDST2191107556188375561973STAT392344174048978840491411

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=42)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr10:75565424-75565424p.R556H3
chr10:75567375-75567375p.R258C2
chr10:75565368-75565368p.Q575E2
chr10:75567378-75567378p.L257I2
chr10:75565745-75565745p.I492M2
chr10:75564621-75564621p.C585R1
chr10:75567575-75567575p.L191fs*121
chr10:75562318-75562318p.T848M1
chr10:75566216-75566216p.T422M1
chr10:75567759-75567759p.N130D1

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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
# sample2 29  3 2  1034 14719
# mutation2 27  3 2  1134 147111
nonsynonymous SNV1 16  2 2  924 125110
synonymous SNV1 11  1    21   22 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
chr10:75567378p.L257I3
chr10:75567302p.R73Q2
chr10:75565368p.Q575E2
chr10:75567929p.H282R2
chr10:75565704p.R744H1
chr10:75568098p.L557I1
chr10:75562762p.R258R1
chr10:75567217p.P740T1
chr10:75563696p.M526I1
chr10:75567627p.R258H1

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 NDST2 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 NDST2

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

AGAP5,ANXA7,AP3M1,BMS1P4,C20orf194,CAMK2G,CHD2,
CLCN6,DNAH1,ECD,FAM149B1,FUT11,ZSWIM8,NDST2,
NPHP3,NUDT13,PPP3CB,RUFY2,SEC24C,TSSK4,USP54
ALPK1,ANGEL1,CTC1,PROSER3,CBFA2T2,CUL9,LINC01000,
GGA3,HPS4,IP6K1,CLUHP3,LDB1,LOC283314,MAML1,
NDST2,PCNXL2,RPL32P3,SLC24A1,SYNGAP1,ZNF785,ZNF862

ARHGAP30,ARHGEF6,CSF2RB,DOCK10,DOCK2,GAB3,GIMAP6,
GIMAP8,HCLS1,IL10RA,ZSWIM8,RIC1,LILRB1,MPEG1,
NDST2,PIK3R5,RAPGEF1,SFMBT2,STAB1,WIPF1,ZMIZ1
ADCY7,ADORA2A,ANKZF1,CBFA2T3,CBX4,CD4,CYTH4,
FHOD1,GAB3,HPS4,IL10RA,NAIP,NDST2,PIK3R6,
PLCB2,PLXNC1,RIMBP3,SETDB1,SIGLEC6,TBC1D2B,TUT1
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 NDST2


There's no related Drug.
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Cross referenced IDs for NDST2
* 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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