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

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 ARSB

Basic gene info.	Gene symbol	ARSB
	Gene name	arylsulfatase B
	Synonyms	ASB\|G4S\|MPS6
	Cytomap	UCSC genome browser: 5q14.1
	Genomic location	chr5 :78073036-78282357
	Type of gene	protein-coding
	RefGenes	NM_000046.3, NM_198709.2,
	Ensembl id	ENSG00000113273
	Description	N-acetylgalactosamine-4-sulfatase
	Modification date	20141207
dbXrefs	MIM : 611542
	HGNC : HGNC
	Ensembl : ENSG00000113273
	HPRD : 08358
	Vega : OTTHUMG00000108129
Protein	UniProt: P15848 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ARSB
	BioGPS: 411
	Gene Expression Atlas: ENSG00000113273
	The Human Protein Atlas: ENSG00000113273
Pathway	NCI Pathway Interaction Database: ARSB
	KEGG: ARSB
	REACTOME: ARSB
	ConsensusPathDB
	Pathway Commons: ARSB
Metabolism	MetaCyc: ARSB
	HUMANCyc: ARSB
Regulation	Ensembl's Regulation: ENSG00000113273
	miRBase: chr5 :78,073,036-78,282,357
	TargetScan: NM_000046
	cisRED: ENSG00000113273
Context	iHOP: ARSB
	cancer metabolism search in PubMed: ARSB
	UCL Cancer Institute: ARSB
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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

Cancer Description
Cancer	CGAP: ARSB
	Familial Cancer Database: ARSB

* 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_GLYCOSPHINGOLIPID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_PROTEINS REACTOME_SPHINGOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS REACTOME_METABOLISM_OF_CARBOHYDRATES

Others
OMIM	253200; phenotype. 272200; phenotype. 611542; gene.
Orphanet	276212; Mucopolysaccharidosis type 6, rapidly progressing. 276223; Mucopolysaccharidosis type 6, slowly progressing.
Disease	KEGG Disease: ARSB
	MedGen: ARSB (Human Medical Genetics with Condition)
	ClinVar: ARSB
Phenotype	MGI: ARSB (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ARSB

Mutations for ARSB

* 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

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- 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

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	ARSB	chr5	78142562	78142582	ARSB	chr5	78142622	78142642
pancreas	ARSB	chr5	78114153	78114173	ARSB	chr5	78113989	78114009
pancreas	ARSB	chr5	78118630	78118830	GRTP1	chr13	114011172	114011372
pancreas	ARSB	chr5	78258929	78258949	ARHGEF37	chr5	148961386	148961406

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 ARSB 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
BP424812	ARSB	220	252	5	78231105	78231212	NALCN	251	277	13	102045709	102045736
AW236827	ARSB	1	369	5	78073039	78073407	DENND2A	367	484	7	140293273	140293390

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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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)

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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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=41)	Stat. for Synonymous SNVs (# total SNVs=7)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	There's no inserted snv.

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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
chr5:78077685-78077685	p.T442T	3
chr5:78076339-78076339	p.V495I	3
chr5:78181442-78181442	p.K369N	2
chr5:78181507-78181507	p.I348F	2
chr5:78077750-78077750	p.E421Q	2
chr5:78260315-78260315	p.G205V	2
chr5:78135201-78135201	p.P397P	2
chr5:78181569-78181569	p.R327Q	2
chr5:78181573-78181573	p.V326I	2
chr5:78076421-78076421	p.P468fs*>66	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	3	4		11			1		2			4	1	1			4	4		6
# mutation	3	4		12			1		2			4	1	1			4	4		6
nonsynonymous SNV	2	4		9			1		2			4	1				1	4		5
synonymous SNV	1			3										1			3			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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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
chr5:78181573	p.G205E,ARSB	2
chr5:78260315	p.V326I,ARSB	2
chr5:78076471	p.A431T	1
chr5:78181629	p.E243G,ARSB	1
chr5:78076234	p.P397L,ARSB	1
chr5:78260317	p.L234I,ARSB	1
chr5:78077720	p.D396D,ARSB	1
chr5:78181641	p.K230K,ARSB	1
chr5:78076243	p.E382K,ARSB	1
chr5:78260357	p.A219D,ARSB	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 ARSB 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 ARSB

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))

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CNV 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

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


ANTXR1,ARSB,C14orf37,CDH11,CHSY3,COL12A1,COL5A2, DPYSL3,DSE,FAM26E,FBN1,FSTL1,LHFPL2,LOX, LUM,MXRA5,NID2,PLXNC1,PRRX1,TIMP2,VCAN	ADAMTS6,ARSB,BCAT1,CALU,CCR1,CD200R1,CMKLR1, CYBB,DAB2,FBN1,FSTL1,LGI2,LILRB5,MPEG1, MPP1,MRC1,MS4A6A,SIGLEC1,SLC36A1,VCAN,XPNPEP2

ARHGAP31,ARSB,ATP8B2,CD93,COL4A2,ENG,FAM101B, FSTL1,FZD4,GNB4,HEG1,LAMC1,PCDH12,PLVAP, PLXDC2,RASD1,RECK,SYNE1,TCF4,TRAM2,ZEB2	ARHGAP31,ARMCX3,ARSB,C17orf51,CCDC149,CEP170,DHX57, FAM120C,FAM161A,FAM178A,FTO,IRS1,KIRREL,MAP3K3, NCDN,PHF19,PPM1F,SETD7,SMAD9,TULP3,UBFD1

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

: Open all plots for all cancer types

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Interacting 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 ARSB

There's no related Drug.

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Cross referenced IDs for ARSB

* 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