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 ARSA

Basic gene info.	Gene symbol	ARSA
	Gene name	arylsulfatase A
	Synonyms	MLD
	Cytomap	UCSC genome browser: 22q13.33
	Genomic location	chr22 :51061181-51066601
	Type of gene	protein-coding
	RefGenes	NM_000487.5, NM_001085425.2,NM_001085426.2,NM_001085427.2,NM_001085428.2,
	Ensembl id	ENSG00000100299
	Description	ASAcerebroside-sulfatase
	Modification date	20141219
dbXrefs	MIM : 607574
	HGNC : HGNC
	Ensembl : ENSG00000100299
	HPRD : 09617
	Vega : OTTHUMG00000150180
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ARSA
	BioGPS: 410
	Gene Expression Atlas: ENSG00000100299
	The Human Protein Atlas: ENSG00000100299
Pathway	NCI Pathway Interaction Database: ARSA
	KEGG: ARSA
	REACTOME: ARSA
	ConsensusPathDB
	Pathway Commons: ARSA
Metabolism	MetaCyc: ARSA
	HUMANCyc: ARSA
Regulation	Ensembl's Regulation: ENSG00000100299
	miRBase: chr22 :51,061,181-51,066,601
	TargetScan: NM_000487
	cisRED: ENSG00000100299
Context	iHOP: ARSA
	cancer metabolism search in PubMed: ARSA
	UCL Cancer Institute: ARSA
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: ARSA
	Familial Cancer Database: ARSA

* 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
KEGG_SPHINGOLIPID_METABOLISM REACTOME_GLYCOSPHINGOLIPID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_PROTEINS REACTOME_SPHINGOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

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

Mutations for ARSA

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ARSA 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
BF932162	ARSA	1	256	22	51065065	51065319	ARSA	253	336	22	51064666	51065061
BF898639	ARSA	5	201	22	51065838	51066034	ANKLE2	198	408	12	133313420	133313630

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

There's no copy number variation information in COSMIC data for this gene.

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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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=15)	Stat. for Synonymous SNVs (# total SNVs=11)

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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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
chr22:51065135-51065135	p.R246R	2
chr22:51065310-51065310	p.A212A	2
chr22:51063878-51063878	p.D409N	1
chr22:51065999-51065999	p.L70R	1
chr22:51065062-51065062	p.G271R	1
chr22:51065322-51065322	p.H208H	1
chr22:51064416-51064416	p.N352S	1
chr22:51066084-51066084	p.G42R	1
chr22:51065086-51065086	p.L263L	1
chr22:51065360-51065360	p.L196L	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=1

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	1		5	1				1	1		2	2				9	2		2
# mutation	1	1		5	1				1	1		2	2				11	2		2
nonsynonymous SNV	1	1		3						1		1	2							1
synonymous SNV				2	1				1			1					11	2		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
chr22:51064600	p.R301Q,ARSA	1
chr22:51065138	p.Q141Q,ARSA	1
chr22:51064619	p.L299L,ARSA	1
chr22:51065164	p.L70R,ARSA	1
chr22:51064623	p.V278V,ARSA	1
chr22:51065277	p.G271R,ARSA	1
chr22:51063591	p.C504C,ARSA	1
chr22:51064631	p.L263L,ARSA	1
chr22:51065310	p.C502C,ARSA	1
chr22:51063597	p.V260V,ARSA	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 ARSA 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 ARSA

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


ALG12,ARSA,C19orf10,CHKB,CRELD2,DPP7,DENND6B, FKBP2,HDAC10,LMF2,LRPAP1,NAGLU,RAB4B,RABAC1, PPP6R2,SCO2,SDF2L1,SELO,TBC1D22A,TOM1,TRABD	ADAP1,ARSA,ABHD16A,C17orf62,BRAT1,CLCN7,CNPY3, COPE,CORO1B,GAA,GMPPA,LMAN2,LRRC29,NAGK, PQLC2,RAB4B,RHBDD3,SHKBP1,TRADD,UNC93B1,ZDHHC12

ARFGAP3,ARSA,C11orf86,C1orf94,CAPN11,CLDN23,DHRS9, GDPD2,ISG20,FAM214B,LMF2,MMP28,MYPN,PLAC8, POLD4,SDCBP2,SMPD1,TRANK1,TSPAN1,UGT1A4,VSIG1	ACP2,ARSA,CTDP1,DENND1C,DKFZp761E198,GMIP,IL17RE, INF2,LGALS3BP,MAST2,MAST3,MBOAT7,PRKCD,RAB40C, RNPEP,RNPEPL1,SIPA1L3,CAPN15,SPINT1,TMC4,VILL

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 ARSA

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB01800	arylsulfatase A	experimental	N,4-Dihydroxy-N-Oxo-3-(Sulfooxy)Benzenaminium
DB03821	arylsulfatase A	experimental	2-Amino-3-Hydroxy-3-Phosphonooxy-Propionic Acid

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Cross referenced IDs for ARSA

* 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