Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 NDST1
Basic gene info.Gene symbolNDST1
Gene nameN-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1
SynonymsHSST|MRT46|NST1
CytomapUCSC genome browser: 5q33.1
Genomic locationchr5 :149887673-149937773
Type of geneprotein-coding
RefGenesNM_001301063.1,
NM_001543.4,
Ensembl idENSG00000070614
DescriptionHSNST 1N-HSST 1N-heparan sulfate sulfotransferase 1NDST-1[Heparan sulfate]-glucosamine N-sulfotransferase 1bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1glucosaminyl N-deacetylase/N-sulfotransferase 1heparan sulfate-N-deacetylase/N
Modification date20141222
dbXrefs MIM : 600853
HGNC : HGNC
Ensembl : ENSG00000070614
HPRD : 02912
Vega : OTTHUMG00000163572
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NDST1
BioGPS: 3340
Gene Expression Atlas: ENSG00000070614
The Human Protein Atlas: ENSG00000070614
PathwayNCI Pathway Interaction Database: NDST1
KEGG: NDST1
REACTOME: NDST1
ConsensusPathDB
Pathway Commons: NDST1
MetabolismMetaCyc: NDST1
HUMANCyc: NDST1
RegulationEnsembl's Regulation: ENSG00000070614
miRBase: chr5 :149,887,673-149,937,773
TargetScan: NM_001301063
cisRED: ENSG00000070614
ContextiHOP: NDST1
cancer metabolism search in PubMed: NDST1
UCL Cancer Institute: NDST1
Assigned class in ccmGDBC

Top
Phenotypic Information for NDST1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NDST1
Familial Cancer Database: NDST1
* 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: NDST1
MedGen: NDST1 (Human Medical Genetics with Condition)
ClinVar: NDST1
PhenotypeMGI: NDST1 (International Mouse Phenotyping Consortium)
PhenomicDB: NDST1

Mutations for NDST1
* 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 NDST1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BU631743FAM168B245332131809603131810549NDST15317085149937242149937419

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
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)

Top
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=4

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=60)
Stat. for Synonymous SNVs
(# total SNVs=32)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

Top
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
chr5:149907676-149907676p.G275D2
chr5:149925000-149925000p.V699V2
chr5:149914445-149914445p.D371D2
chr5:149915419-149915419p.R470H2
chr5:149925012-149925012p.L703L2
chr5:149932797-149932797p.Y851C2
chr5:149922503-149922503p.N647S2
chr5:149932804-149932804p.R853R2
chr5:149918810-149918810p.C486C2
chr5:149901260-149901260p.D148D2

Top
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
# sample13 102 2 2  843  1013 16
# mutation13 102 2 2  943  1016 19
nonsynonymous SNV   7  1 2  641  411 12
synonymous SNV13 32 1    3 2  65 7
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])

Top
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
chr5:149924914p.R470H2
chr5:149915419p.D671N2
chr5:149914445p.D371D2
chr5:149927842p.A430A1
chr5:149900850p.C586F1
chr5:149914501p.E762K1
chr5:149918868p.D58Y1
chr5:149931403p.E247Q1
chr5:149901143p.G435G1
chr5:149921221p.E598K1

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 NDST1 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]

Top
Gene Expression for NDST1

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

ADCY6,ARHGEF37,PRRC2B,BTBD7,FAM13B,FAM172A,GALNT10,
ARHGAP35,KDM3B,KIF13B,LOC100129034,MTHFR,NDST1,PCDH1,
PDPK1,PRICKLE2,RREB1,SAP30L,TECPR2,VPS13D,ZNF106
ACVR1B,PRRC2B,DZANK1,CGNL1,CUL9,SPECC1L,ARHGAP35,
IP6K1,LDOC1L,NDST1,PACSIN2,PFAS,PITPNM3,PLEKHA7,
SNRNP200,SRCAP,TATDN2,TBC1D14,TECPR2,TMEM63A,TTC22

AFAP1L1,CD93,COL4A1,COL4A2,ENG,FLT4,GPR124,
HEG1,HSPG2,KDR,LAMA4,MMRN2,NDST1,NID1,
STAB1,STARD8,THBD,TIE1,VASH1,ZEB2,ZNF366
ELMSAN1,CCDC85C,DNAJC5,ARHGAP35,IGSF3,KSR1,LAMP1,
MED15,NDST1,NFE2L1,NIPAL3,OTUD7B,PLXNB2,SORT1,
STAU1,SYNPO,USP9X,VPS18,ZER1,ZFAND3,ZMIZ1
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for NDST1
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
DB01812N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1experimentalAdenosine-3'-5'-Diphosphate


Top
Cross referenced IDs for NDST1
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas