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 CHST5
Basic gene info.Gene symbolCHST5
Gene namecarbohydrate (N-acetylglucosamine 6-O) sulfotransferase 5
SynonymsI-GlcNAc-6-ST|I-GlcNAc6ST|glcNAc6ST-3|gn6st-3|hIGn6ST
CytomapUCSC genome browser: 16q22.3
Genomic locationchr16 :75562427-75569068
Type of geneprotein-coding
RefGenesNM_024533.4,
NM_012126.1,
Ensembl idENSG00000135702
DescriptionGST4-alphaN-acetylglucosamine 6-O-sulfotransferase 3carbohydrate sulfotransferase 5galactose/N-acetylglucosamine/N-acetylglucosamine 6-O-sulfotransferase 4-alphaintestinal GlcNAc-6-sulfotransferase
Modification date20141207
dbXrefs MIM : 604817
HGNC : HGNC
Ensembl : ENSG00000135702
HPRD : 07059
Vega : OTTHUMG00000137610
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CHST5
BioGPS: 23563
Gene Expression Atlas: ENSG00000135702
The Human Protein Atlas: ENSG00000135702
PathwayNCI Pathway Interaction Database: CHST5
KEGG: CHST5
REACTOME: CHST5
ConsensusPathDB
Pathway Commons: CHST5
MetabolismMetaCyc: CHST5
HUMANCyc: CHST5
RegulationEnsembl's Regulation: ENSG00000135702
miRBase: chr16 :75,562,427-75,569,068
TargetScan: NM_024533
cisRED: ENSG00000135702
ContextiHOP: CHST5
cancer metabolism search in PubMed: CHST5
UCL Cancer Institute: CHST5
Assigned class in ccmGDBC

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Phenotypic Information for CHST5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CHST5
Familial Cancer Database: CHST5
* 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: CHST5
MedGen: CHST5 (Human Medical Genetics with Condition)
ClinVar: CHST5
PhenotypeMGI: CHST5 (International Mouse Phenotyping Consortium)
PhenomicDB: CHST5

Mutations for CHST5
* 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 CHST5 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AK075034ABHD14B399035200320052008065CHST59881673167557220275572887

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=7

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=47)
Stat. for Synonymous SNVs
(# total SNVs=20)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr16:75563330-75563330p.T318M5
chr16:75563746-75563746p.P179P3
chr16:75564025-75564025p.P86P3
chr16:75563490-75563490p.R265C2
chr16:75563963-75563963p.A107V2
chr16:75563999-75563999p.A95V2
chr16:75563927-75563927p.R119H2
chr16:75563329-75563329p.T318T2
chr16:75563756-75563756p.T176M2
chr16:75563653-75563653p.L210L1

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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
# sample 1165 2 1  861  10918
# mutation 1165 3 1  861  91118
nonsynonymous SNV 1161 2    75   6817
synonymous SNV    4 1 1  111  33 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
chr16:75563756p.T176M2
chr16:75563963p.R265C2
chr16:75563644p.P213P2
chr16:75563490p.A107V2
chr16:75563946p.G79S1
chr16:75563388p.A372T1
chr16:75564134p.G163D1
chr16:75563598p.G74V1
chr16:75563169p.C371C1
chr16:75563417p.W254S1

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 CHST5 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 CHST5

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

ACD,AGAP3,ENKD1,SPATA33,H1FX-AS1,SAPCD1,CDK10,
CENPT,CHST5,GLI4,KIFC2,PRR22,PRR7,QTRT1,
RPL13,SLMO1,SPG7,TAF1C,TMEM231,TRMT1,ZNF579
ANO9,C1orf159,CCDC24,CHST5,DGCR8,DTX3,EBF4,
DENND6B,IFT27,PRR22,PRRT1,RCE1,RHBDF1,RTKN,
SAMD10,SERINC2,SH3GLB2,SLC25A29,TMEM198,TSEN54,ZNF574

ATP2A3,B3GALT5,BCAS1,CAPN9,CHST5,CREB3L1,FABP2,
FER1L6,KLF4,KLK1,LRRIQ4,MARVELD3,MUC2,REG4,
ST6GALNAC1,TMEM61,TMEM92,TPSG1,TSPAN1,VWA3B,ZBTB7C
B3GNT7,PRAC2,CAPN13,CDHR1,CHST5,FOXA2,GMCL1,
GPRIN2,HOXB13,LOC284578,MFI2,MFSD4,MMP28,MNX1,
PP14571,PRAC1,QPRT,SIDT1,SPON1,ST6GALNAC6,TMCO3
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 CHST5


There's no related Drug.
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Cross referenced IDs for CHST5
* 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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