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 CHST15
Basic gene info.Gene symbolCHST15
Gene namecarbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15
SynonymsBRAG|GALNAC4S-6ST
CytomapUCSC genome browser: 10q26
Genomic locationchr10 :125779168-125851930
Type of geneprotein-coding
RefGenesNM_001270764.1,
NM_001270765.1,NM_014863.3,NM_015892.4,
Ensembl idENSG00000182022
DescriptionB cell RAG associated protein (GALNAC4S-6ST)B-cell RAG-associated gene proteincarbohydrate sulfotransferase 15hBRAG
Modification date20141207
dbXrefs MIM : 608277
HGNC : HGNC
Ensembl : ENSG00000182022
HPRD : 12203
Vega : OTTHUMG00000019208
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CHST15
BioGPS: 51363
Gene Expression Atlas: ENSG00000182022
The Human Protein Atlas: ENSG00000182022
PathwayNCI Pathway Interaction Database: CHST15
KEGG: CHST15
REACTOME: CHST15
ConsensusPathDB
Pathway Commons: CHST15
MetabolismMetaCyc: CHST15
HUMANCyc: CHST15
RegulationEnsembl's Regulation: ENSG00000182022
miRBase: chr10 :125,779,168-125,851,930
TargetScan: NM_001270764
cisRED: ENSG00000182022
ContextiHOP: CHST15
cancer metabolism search in PubMed: CHST15
UCL Cancer Institute: CHST15
Assigned class in ccmGDBC

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Phenotypic Information for CHST15(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CHST15
Familial Cancer Database: CHST15
* 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: CHST15
MedGen: CHST15 (Human Medical Genetics with Condition)
ClinVar: CHST15
PhenotypeMGI: CHST15 (International Mouse Phenotyping Consortium)
PhenomicDB: CHST15

Mutations for CHST15
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryCHST15chr10125843544125843564chr206101547261015492
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 CHST15 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE707961CHST1517419910125804446125804472ISLR193407157446827074468481
BE830532CHST15521710125768238125768450RBM4B211408116643829566438492

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        
GAIN (# sample)        1        
LOSS (# sample)                 
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=56)
Stat. for Synonymous SNVs
(# total SNVs=24)
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
chr10:125805533-125805533p.E66*5
chr10:125780896-125780896p.S408L3
chr10:125769742-125769742p.R537W2
chr10:125805345-125805345p.P128P2
chr10:125801922-125801922p.V310M2
chr10:125805353-125805353p.E126K2
chr10:125801930-125801930p.R307L2
chr10:125805389-125805389p.G114R2
chr10:125804259-125804259p.A241A2
chr10:125804267-125804267p.H239N2

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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 1 19  2 1  611  98 10
# mutation 1 20  2 1  711  109 11
nonsynonymous SNV 1 15  2 1  41   76 4
synonymous SNV   5       3 1  33 7
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
chr10:125805533p.E66K,CHST153
chr10:125769742p.E126K,CHST152
chr10:125805511p.G114R,CHST152
chr10:125798163p.R537W,CHST152
chr10:125805353p.R477C,CHST152
chr10:125771915p.R73H,CHST152
chr10:125805389p.W353L,CHST152
chr10:125805483p.D553D,CHST151
chr10:125798145p.R436R,CHST151
chr10:125804216p.H276Y,CHST151

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 CHST15 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 CHST15

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 CHST15


There's no related Drug.
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Cross referenced IDs for CHST15
* 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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