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 CHST2
Basic gene info.Gene symbolCHST2
Gene namecarbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2
SynonymsC6ST|GST-2|GST2|Gn6ST-1|HEL-S-75|glcNAc6ST-1
CytomapUCSC genome browser: 3q24
Genomic locationchr3 :142838617-142842856
Type of geneprotein-coding
RefGenesNM_004267.4,
Ensembl idENSG00000175040
DescriptionN-acetylglucosamine 6-O-sulfotransferase 1carbohydrate (chondroitin 6/keratan) sulfotransferase 2carbohydrate sulfotransferase 2epididymis secretory protein Li 75galactose/N-acetylglucosamine/N-acetylglucosamine 6-O-sulfotransferase 2
Modification date20141207
dbXrefs MIM : 603798
HGNC : HGNC
Ensembl : ENSG00000175040
HPRD : 04814
Vega : OTTHUMG00000159351
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CHST2
BioGPS: 9435
Gene Expression Atlas: ENSG00000175040
The Human Protein Atlas: ENSG00000175040
PathwayNCI Pathway Interaction Database: CHST2
KEGG: CHST2
REACTOME: CHST2
ConsensusPathDB
Pathway Commons: CHST2
MetabolismMetaCyc: CHST2
HUMANCyc: CHST2
RegulationEnsembl's Regulation: ENSG00000175040
miRBase: chr3 :142,838,617-142,842,856
TargetScan: NM_004267
cisRED: ENSG00000175040
ContextiHOP: CHST2
cancer metabolism search in PubMed: CHST2
UCL Cancer Institute: CHST2
Assigned class in ccmGDBC

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Phenotypic Information for CHST2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CHST2
Familial Cancer Database: CHST2
* 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: CHST2
MedGen: CHST2 (Human Medical Genetics with Condition)
ClinVar: CHST2
PhenotypeMGI: CHST2 (International Mouse Phenotyping Consortium)
PhenomicDB: CHST2

Mutations for CHST2
* 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 CHST2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ188039CLN6157156849935068499406CHST2521633142841558142841670
BQ185214CHST2172713142841558142841812CLN6266322156849935068499406

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 # sample    1 2          
GAIN (# sample)    1            
LOSS (# sample)      2          
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=61)
Stat. for Synonymous SNVs
(# total SNVs=15)
Stat. for Deletions
(# total SNVs=2)
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
chr3:142840164-142840164p.V169A2
chr3:142840978-142840978p.Y440*2
chr3:142840772-142840772p.A372T2
chr3:142840774-142840774p.A372A2
chr3:142840311-142840311p.D218V2
chr3:142841059-142841059p.K467N2
chr3:142840332-142840332p.R225H2
chr3:142841089-142841089p.T477T2
chr3:142840277-142840277p.G207W2
chr3:142840752-142840752p.R365H2

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample24 162 2 1  8561151113
# mutation24 182 2 1  8561161213
nonsynonymous SNV12 142 2 1  7551 41012
synonymous SNV12 4       1 1 122 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
chr3:142840774p.S401N2
chr3:142841171p.V505I2
chr3:142840860p.A372A2
chr3:142840212p.F191L1
chr3:142840752p.F309F1
chr3:142840454p.K379R1
chr3:142840921p.K467N1
chr3:142840619p.W201L1
chr3:142841109p.A312T1
chr3:142840223p.G385S1

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 CHST2 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 CHST2

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

THEMIS2,CD38,CD97,CHST2,FAM26F,HLA-DOB,HLA-F,
ICAM4,IL12RB1,ITM2C,LAG3,MOB3B,MSLN,NCF4,
NCK1,RASSF4,RELB,REM1,SH3KBP1,SPIB,UBD
AURKB,CDT1,CDX1,CHST2,CKAP4,CSK,FCHO1,
FSCN1,HAPLN3,IKBKE,IL27RA,LIMK1,LMNB2,NT5DC2,
PITPNM1,RELB,SEMA7A,SH3BP1,TACC3,TMEM158,TSPAN33

ADORA2A,ARHGEF6,CHST2,CSF2RB,DOCK2,FAM78A,FLI1,
FMNL1,GAB3,GIMAP4,GIMAP6,GMFG,HCLS1,IL10RA,
KCNN3,PIK3R5,RASSF2,RCSD1,SLAMF1,WAS,WIPF1
C1orf186,CCL22,CCR8,CD80,CHST2,CSF2RB,CTLA4,
EMR2,IL4I1,ITGAX,KRT37,LILRB1,MMP9,PDE4B,
PLA2G7,RASSF5,RELT,SEMA4A,SLC16A6,TNFRSF4,TRPV2
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 CHST2


There's no related Drug.
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Cross referenced IDs for CHST2
* 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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