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 ARSB
Basic gene info.Gene symbolARSB
Gene namearylsulfatase B
SynonymsASB|G4S|MPS6
CytomapUCSC genome browser: 5q14.1
Genomic locationchr5 :78073036-78282357
Type of geneprotein-coding
RefGenesNM_000046.3,
NM_198709.2,
Ensembl idENSG00000113273
DescriptionN-acetylgalactosamine-4-sulfatase
Modification date20141207
dbXrefs MIM : 611542
HGNC : HGNC
Ensembl : ENSG00000113273
HPRD : 08358
Vega : OTTHUMG00000108129
ProteinUniProt: P15848
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ARSB
BioGPS: 411
Gene Expression Atlas: ENSG00000113273
The Human Protein Atlas: ENSG00000113273
PathwayNCI Pathway Interaction Database: ARSB
KEGG: ARSB
REACTOME: ARSB
ConsensusPathDB
Pathway Commons: ARSB
MetabolismMetaCyc: ARSB
HUMANCyc: ARSB
RegulationEnsembl's Regulation: ENSG00000113273
miRBase: chr5 :78,073,036-78,282,357
TargetScan: NM_000046
cisRED: ENSG00000113273
ContextiHOP: ARSB
cancer metabolism search in PubMed: ARSB
UCL Cancer Institute: ARSB
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for ARSB(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic 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

check002.gifOthers
OMIM 253200; phenotype.
272200; phenotype.
611542; gene.
Orphanet 276212; Mucopolysaccharidosis type 6, rapidly progressing.
276223; Mucopolysaccharidosis type 6, slowly progressing.
DiseaseKEGG Disease: ARSB
MedGen: ARSB (Human Medical Genetics with Condition)
ClinVar: ARSB
PhenotypeMGI: ARSB (International Mouse Phenotyping Consortium)
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.

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
* 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryARSBchr57814256278142582ARSBchr57814262278142642
pancreasARSBchr57811415378114173ARSBchr57811398978114009
pancreasARSBchr57811863078118830GRTP1chr13114011172114011372
pancreasARSBchr57825892978258949ARHGEF37chr5148961386148961406
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 ARSB related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BP424812ARSB22025257823110578231212NALCN25127713102045709102045736
AW236827ARSB136957807303978073407DENND2A3674847140293273140293390

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      3         1
GAIN (# sample)                 
LOSS (# sample)      3         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=3

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check002.gifSomatic 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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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
chr5:78076339-78076339p.V495I3
chr5:78077685-78077685p.T442T3
chr5:78181507-78181507p.I348F2
chr5:78077750-78077750p.E421Q2
chr5:78260315-78260315p.G205V2
chr5:78135201-78135201p.P397P2
chr5:78181569-78181569p.R327Q2
chr5:78181573-78181573p.V326I2
chr5:78181442-78181442p.K369N2
chr5:78181490-78181490p.W353C1

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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
# sample34 11  1 2  411  44 6
# mutation34 12  1 2  411  44 6
nonsynonymous SNV24 9  1 2  41   14 5
synonymous SNV1  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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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
chr5:78181573p.G205E,ARSB2
chr5:78260315p.V326I,ARSB2
chr5:78251156p.L30M,ARSB1
chr5:78076321p.R479W1
chr5:78260426p.N292S,ARSB1
chr5:78135248p.D478N1
chr5:78251159p.S287N,ARSB1
chr5:78076339p.D476N1
chr5:78264838p.S286N,ARSB1
chr5:78181427p.S271S,ARSB1

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 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

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

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
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 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



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