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 CHST6
Basic gene info.Gene symbolCHST6
Gene namecarbohydrate (N-acetylglucosamine 6-O) sulfotransferase 6
SynonymsMCDC1
CytomapUCSC genome browser: 16q22
Genomic locationchr16 :75507021-75528926
Type of geneprotein-coding
RefGenesNM_021615.4,
Ensembl idENSG00000183196
DescriptionC-GlcNAc6STGST4-betaN-acetylglucosamine 6-O-sulfotransferase 5carbohydrate sulfotransferase 6corneal N-acetylglucosamine 6-sulfotransferasecorneal N-acetylglucosamine-6-O-sulfotransferasegalactose/N-acetylglucosamine/N-acetylglucosamine 6-O-sulfotra
Modification date20141207
dbXrefs MIM : 605294
HGNC : HGNC
Ensembl : ENSG00000183196
HPRD : 05597
Vega : OTTHUMG00000137612
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CHST6
BioGPS: 4166
Gene Expression Atlas: ENSG00000183196
The Human Protein Atlas: ENSG00000183196
PathwayNCI Pathway Interaction Database: CHST6
KEGG: CHST6
REACTOME: CHST6
ConsensusPathDB
Pathway Commons: CHST6
MetabolismMetaCyc: CHST6
HUMANCyc: CHST6
RegulationEnsembl's Regulation: ENSG00000183196
miRBase: chr16 :75,507,021-75,528,926
TargetScan: NM_021615
cisRED: ENSG00000183196
ContextiHOP: CHST6
cancer metabolism search in PubMed: CHST6
UCL Cancer Institute: CHST6
Assigned class in ccmGDBC

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Phenotypic Information for CHST6(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CHST6
Familial Cancer Database: CHST6
* 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: CHST6
MedGen: CHST6 (Human Medical Genetics with Condition)
ClinVar: CHST6
PhenotypeMGI: CHST6 (International Mouse Phenotyping Consortium)
PhenomicDB: CHST6

Mutations for CHST6
* 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 CHST6 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AF219990CHST612069167551235075529282COTL120702521168459920284599653

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=56)
Stat. for Synonymous SNVs
(# total SNVs=13)
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
chr16:75513386-75513386p.R114H3
chr16:75513561-75513561p.V56M3
chr16:75512546-75512546p.R394Q3
chr16:75512762-75512762p.S322L3
chr16:75513562-75513562p.F55F2
chr16:75512725-75512725p.R334R2
chr16:75513568-75513568p.S53S2
chr16:75512862-75512862p.A289T2
chr16:75512732-75512732p.A332V2
chr16:75513330-75513330p.P133T2

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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
# sample3 182 12   17511 710 7
# mutation3 172 12   17511 711 10
nonsynonymous SNV1 152 6   15511 49 6
synonymous SNV2  2  6    2    32 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
chr16:75512725p.R334R3
chr16:75512895p.R278W2
chr16:75512732p.E274K2
chr16:75512907p.A73A2
chr16:75513508p.A332V2
chr16:75512862p.F55F2
chr16:75513562p.A289T2
chr16:75513474p.G382D1
chr16:75513075p.P280P1
chr16:75513666p.I197S1

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 CHST6 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 CHST6

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

BAG2,C17orf51,CALU,CHST3,CHST6,DLX6,DLX6AS,
FAT1,FOXL1,GLG1,GLS,MAML2,MDFI,MET,
MICALL1,PLOD1,PTK7,RAB23,SFT2D2,SOX6,UCA1
ADAM8,ATP6V0D2,BEAN,CD300LF,CHST11,CHST6,CNGB1,
DGKA,GAL3ST4,HTRA4,IKBKE,LILRA4,PITPNM1,PKD2L1,
SDS,SH3BP1,SLC38A5,TMEM51,TNC,UBASH3B,UNC13D

B3GNT9,C11orf24,TMEM263,CHST6,CREB3L1,FAM114A1,FUT8,
GAS2L1,GJB5,GPX8,HIF1A,IKBIP,KCNK6,KDELR3,
PDE4D,RELL1,SEC24D,SEMA4B,SIX4,SLC16A2,TANC2
ABHD12,C10orf54,C1orf115,CCL14-CCL15,CDHR5,CHST6,EPS8L2,
FAM102A,INPP5J,KIAA1211,KIAA2013,LOC151534,MEP1A,NGEF,
PC,PDLIM2,PLA2G12B,RIN2,RIPK4,TMEM120A,TMEM150B
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 CHST6


There's no related Drug.
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Cross referenced IDs for CHST6
* 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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