Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 symbol	CHST15
	Gene name	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15
	Synonyms	BRAG\|GALNAC4S-6ST
	Cytomap	UCSC genome browser: 10q26
	Genomic location	chr10 :125779168-125851930
	Type of gene	protein-coding
	RefGenes	NM_001270764.1, NM_001270765.1,NM_014863.3,NM_015892.4,
	Ensembl id	ENSG00000182022
	Description	B cell RAG associated protein (GALNAC4S-6ST)B-cell RAG-associated gene proteincarbohydrate sulfotransferase 15hBRAG
	Modification date	20141207
dbXrefs	MIM : 608277
	HGNC : HGNC
	Ensembl : ENSG00000182022
	HPRD : 12203
	Vega : OTTHUMG00000019208
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CHST15
	BioGPS: 51363
	Gene Expression Atlas: ENSG00000182022
	The Human Protein Atlas: ENSG00000182022
Pathway	NCI Pathway Interaction Database: CHST15
	KEGG: CHST15
	REACTOME: CHST15
	ConsensusPathDB
	Pathway Commons: CHST15
Metabolism	MetaCyc: CHST15
	HUMANCyc: CHST15
Regulation	Ensembl's Regulation: ENSG00000182022
	miRBase: chr10 :125,779,168-125,851,930
	TargetScan: NM_001270764
	cisRED: ENSG00000182022
Context	iHOP: CHST15
	cancer metabolism search in PubMed: CHST15
	UCL Cancer Institute: CHST15
Assigned class in ccmGDB	C

Top

Phenotypic Information for CHST15(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_CARBOHYDRATES

Others
OMIM
Orphanet
Disease	KEGG Disease: CHST15
	MedGen: CHST15 (Human Medical Genetics with Condition)
	ClinVar: CHST15
Phenotype	MGI: CHST15 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

Top

- 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.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	CHST15	chr10	125843544	125843564		chr20	61015472	61015492

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CHST15 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
BE707961	CHST15	174	199	10	125804446	125804472	ISLR	193	407	15	74468270	74468481
BE830532	CHST15	5	217	10	125768238	125768450	RBM4B	211	408	11	66438295	66438492

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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)

Top

SNV 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

Top

Somatic 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)

Top

Top 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 position	Mutation(aa)	Unique sampleID count
chr10:125805533-125805533	p.E66*	5
chr10:125780896-125780896	p.S408L	3
chr10:125804259-125804259	p.A241A	2
chr10:125804267-125804267	p.H239N	2
chr10:125798163-125798163	p.W353L	2
chr10:125769742-125769742	p.R537W	2
chr10:125805345-125805345	p.P128P	2
chr10:125801922-125801922	p.V310M	2
chr10:125805353-125805353	p.E126K	2
chr10:125801930-125801930	p.R307L	2

Top

SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample		1		19			2		1			6	1	1			9	8		10
# mutation		1		20			2		1			7	1	1			10	9		11
nonsynonymous SNV		1		15			2		1			4	1				7	6		4
synonymous SNV				5								3		1			3	3		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])

Top

Top 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 Position	Mutation(aa)	Unique sampleID count
chr10:125805533	p.E66K,CHST15	3
chr10:125805353	p.R537W,CHST15	2
chr10:125771915	p.R477C,CHST15	2
chr10:125805389	p.W353L,CHST15	2
chr10:125769742	p.R73H,CHST15	2
chr10:125798163	p.E126K,CHST15	2
chr10:125805511	p.G114R,CHST15	2
chr10:125804267	p.H242H,CHST15	1
chr10:125769829	p.F111F,CHST15	1
chr10:125780811	p.S411S,CHST15	1

Other 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

Copy 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]

Top

Gene Expression for CHST15

Gene 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.

Differential 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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

Gene-Gene Network Information

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for CHST15

There's no related Drug.

Top

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