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 NDST4
Basic gene info.Gene symbolNDST4
Gene nameN-deacetylase/N-sulfotransferase (heparan glucosaminyl) 4
SynonymsNDST-4|NHSST4
CytomapUCSC genome browser: 4q26
Genomic locationchr4 :115748926-116035032
Type of geneprotein-coding
RefGenesNM_022569.1,
Ensembl idENSG00000138653
DescriptionN-HSST 4N-heparan sulfate sulfotransferase 4bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 4glucosaminyl N-deacetylase/N-sulfotransferase 4
Modification date20141207
dbXrefs MIM : 615039
HGNC : HGNC
Ensembl : ENSG00000138653
HPRD : 10116
Vega : OTTHUMG00000132916
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NDST4
BioGPS: 64579
Gene Expression Atlas: ENSG00000138653
The Human Protein Atlas: ENSG00000138653
PathwayNCI Pathway Interaction Database: NDST4
KEGG: NDST4
REACTOME: NDST4
ConsensusPathDB
Pathway Commons: NDST4
MetabolismMetaCyc: NDST4
HUMANCyc: NDST4
RegulationEnsembl's Regulation: ENSG00000138653
miRBase: chr4 :115,748,926-116,035,032
TargetScan: NM_022569
cisRED: ENSG00000138653
ContextiHOP: NDST4
cancer metabolism search in PubMed: NDST4
UCL Cancer Institute: NDST4
Assigned class in ccmGDBC

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Phenotypic Information for NDST4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NDST4
Familial Cancer Database: NDST4
* 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: NDST4
MedGen: NDST4 (Human Medical Genetics with Condition)
ClinVar: NDST4
PhenotypeMGI: NDST4 (International Mouse Phenotyping Consortium)
PhenomicDB: NDST4

Mutations for NDST4
* 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
breastNDST4chr4115981060115981460SLC25A29chr14100771204100771604
pancreasNDST4chr4115801627115801827NDST4chr4115795448115795648
pancreasNDST4chr4116003076116003096chr115544108455441104
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 NDST4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
U47050NDST411604116034598116034757TRPC315634164122800183122854200

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 # sample21 1  2   1      
GAIN (# sample)1     1          
LOSS (# sample)11 1  1   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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=139)
Stat. for Synonymous SNVs
(# total SNVs=39)
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
chr4:115998159-115998159p.R12*6
chr4:115997885-115997885p.R103Q4
chr4:115891689-115891689p.E373V3
chr4:115998003-115998003p.E64*3
chr4:115997242-115997242p.G317G3
chr4:115754820-115754820p.D780N3
chr4:115997368-115997368p.L275L3
chr4:115891702-115891702p.R369W3
chr4:115769380-115769380p.G644E3
chr4:115858527-115858527p.P452S2

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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=6

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample321155 10 51 33132 43914111
# mutation321155 10 51 38152 45114115
nonsynonymous SNV2 1125 7 5  26112 44012111
synonymous SNV12 3  3  1 124   112 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
chr4:115767138p.G317G3
chr4:115997368p.F652F3
chr4:115769380p.G644E3
chr4:115997242p.L275F3
chr4:115891689p.P452A2
chr4:115997337p.E373V2
chr4:115858492p.R708L2
chr4:115858527p.G317R2
chr4:115760697p.D286N2
chr4:115767075p.S673S2

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 NDST4 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 NDST4

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

ABCB11,ABO,ADCY1,C16orf46,ERICH3,CES4A,CLRN1,
FMO5,GFPT1,GRID2,LRRC36,NDST4,NPAS3,PDZK1P1,
PEX5L,POTEC,POTED,SLC26A5,VRK2,VSTM2A,ZNF19
ACTBL2,C4BPA,CBLN4,CLDN1,DEFB131,FOXR2,GRID2,
GRIK2,HTR1A,LRRC36,NAA11,NDST3,NDST4,NTS,
OR6Y1,PRAMEF11,PRSS48,RAG2,RBMXL3,RGS2,SLC26A2

BANF2,BPIFB2,MIR1-1HG,CLEC2A,EPHA7,BRINP3,KCNJ9,
LOC647309,LRP1B,NDST4,NR0B1,BPIFA1,REG1B,REG3A,
SDC4P,SERPINA11,SERPINA3,SLC5A12,TPTE2P3,TRIM17,ZIC1
ATXN7L3B,LINC00518,CUL4B,EIF3L,GNRHR2,KRT40,FAR2P1,
LRRC39,MATR3,METTL14,MUM1L1,NDST4,PAIP2B,PPP2R5C,
RBM4B,RPL22,SIAH2,TBCK,TMEM67,ZNF615,ZNF830
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 NDST4


There's no related Drug.
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Cross referenced IDs for NDST4
* 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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