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 CHST1
Basic gene info.Gene symbolCHST1
Gene namecarbohydrate (keratan sulfate Gal-6) sulfotransferase 1
SynonymsC6ST|GST-1|KS6ST|KSGal6ST|KSST
CytomapUCSC genome browser: 11p11.2
Genomic locationchr11 :45669238-45687206
Type of geneprotein-coding
RefGenesNM_003654.5,
Ensembl idENSG00000175264
Descriptioncarbohydrate (chondroitin 6/keratan) sulfotransferase 1carbohydrate sulfotransferase 1galactose/N-acetylglucosamine/N-acetylglucosamine 6-O-sulfotransferase 1
Modification date20141207
dbXrefs MIM : 603797
HGNC : HGNC
HPRD : 07051
ProteinUniProt: O43916
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CHST1
BioGPS: 8534
Gene Expression Atlas: ENSG00000175264
The Human Protein Atlas: ENSG00000175264
PathwayNCI Pathway Interaction Database: CHST1
KEGG: CHST1
REACTOME: CHST1
ConsensusPathDB
Pathway Commons: CHST1
MetabolismMetaCyc: CHST1
HUMANCyc: CHST1
RegulationEnsembl's Regulation: ENSG00000175264
miRBase: chr11 :45,669,238-45,687,206
TargetScan: NM_003654
cisRED: ENSG00000175264
ContextiHOP: CHST1
cancer metabolism search in PubMed: CHST1
UCL Cancer Institute: CHST1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for CHST1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CHST1
Familial Cancer Database: CHST1
* 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 603797; gene.
Orphanet
DiseaseKEGG Disease: CHST1
MedGen: CHST1 (Human Medical Genetics with Condition)
ClinVar: CHST1
PhenotypeMGI: CHST1 (International Mouse Phenotyping Consortium)
PhenomicDB: CHST1

Mutations for CHST1
* 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 CHST1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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        11  
GAIN (# sample)              1  
LOSS (# sample)    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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=59)
Stat. for Synonymous SNVs
(# total SNVs=26)
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
chr11:45671251-45671251p.R408H4
chr11:45671602-45671602p.P291L3
chr11:45672345-45672345p.A43A2
chr11:45672090-45672090p.Y128Y2
chr11:45671711-45671711p.R255R2
chr11:45671304-45671304p.S390S2
chr11:45671632-45671632p.N281S2
chr11:45672017-45672017p.R153C2
chr11:45671646-45671646p.C276C2
chr11:45671729-45671729p.D249N2

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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
# sample111162 4    135  11122 13
# mutation111152 4    145  11322 15
nonsynonymous SNV 1 101 3    93   714 10
synonymous SNV1 161 1    52  168 5
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
chr11:45671602p.P291L4
chr11:45671251p.C276C3
chr11:45671646p.R408H3
chr11:45671304p.N281S2
chr11:45671729p.Y128Y2
chr11:45671313p.A43A2
chr11:45671632p.T274T2
chr11:45671749p.G261R2
chr11:45672090p.R113W2
chr11:45671393p.S390S2

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 CHST1 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 CHST1

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

ADAMTS12,AHNAK,APBB2,ATG2B,CREBRF,CASC4,CHST15,
FAM63B,FBN1,FNIP1,FYCO1,EFCAB14,LRRFIP1,MYOF,
PRKG1,SEL1L,SLC24A2,STAM2,TRIM23,ZEB1,ZNF484
AFF3,ARMC9,ARSJ,CHST15,DCAF7,DLGAP1,DRAM1,
FUT8,IGSF3,KIAA0247,LRRC16A,MAGI3,MICALCL,NDE1,
PNMA2,PTPN9,RASEF,ROR2,SHROOM2,TPBG,TSPAN5

ADAM12,CCDC88A,CFH,CHST15,COL6A1,COL6A2,ELK3,
EMP3,GNAI2,PPP1R18,MAFB,MSN,MYO5A,NRP1,
NRP2,PTRF,QKI,ROBO4,SCARF1,SEMA6B,SNAI2
BNC2,CHST15,DIP2C,DMD,FRMPD4,FYCO1,GNAO1,
JMY,MEIS2,NBEA,NRP2,TENM3___TENM1,PEG10,PRICKLE2,
PRUNE2,PTGS1,RNF150,ROR2,TRPS1,TSPYL5,ZNF532
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 CHST1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA26501; -.
Organism-specific databasesCTD 8534; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01033carbohydrate (keratan sulfate Gal-6) sulfotransferase 1approvedMercaptopurine
DB00563carbohydrate (keratan sulfate Gal-6) sulfotransferase 1approvedMethotrexate


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Cross referenced IDs for CHST1
* 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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