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 IDS

Basic gene info.	Gene symbol	IDS
	Gene name	iduronate 2-sulfatase
	Synonyms	MPS2\|SIDS
	Cytomap	UCSC genome browser: Xq28
	Genomic location	chrX :148568661-148586884
	Type of gene	protein-coding
	RefGenes	NM_000202.6, NM_001166550.2,NM_006123.4,NR_104128.1,
	Ensembl id	ENSG00000267816
	Description	alpha-L-iduronate sulfate sulfataseiduronate 2-sulfatase 14 kDa chainiduronate 2-sulfatase 42 kDa chainidursulfase
	Modification date	20141219
dbXrefs	MIM : 300823
	HGNC : HGNC
	Ensembl : ENSG00000010404
	HPRD : 02402
	Vega : OTTHUMG00000022615
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_IDS
	BioGPS: 3423
	Gene Expression Atlas: ENSG00000267816
	The Human Protein Atlas: ENSG00000267816
Pathway	NCI Pathway Interaction Database: IDS
	KEGG: IDS
	REACTOME: IDS
	ConsensusPathDB
	Pathway Commons: IDS
Metabolism	MetaCyc: IDS
	HUMANCyc: IDS
Regulation	Ensembl's Regulation: ENSG00000267816
	miRBase: chrX :148,568,661-148,586,884
	TargetScan: NM_000202
	cisRED: ENSG00000267816
Context	iHOP: IDS
	cancer metabolism search in PubMed: IDS
	UCL Cancer Institute: IDS
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: IDS
	Familial Cancer Database: IDS

* 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: IDS
	MedGen: IDS (Human Medical Genetics with Condition)
	ClinVar: IDS
Phenotype	MGI: IDS (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: IDS

Mutations for IDS

* 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 IDS 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
BP384531	IDS	1	65	X	148564535	148564599	PAIP2	64	376	5	138705082	138705389
BU622671	IDS	18	348	X	148560300	148560630	SNHG3	345	580	1	28835590	28835825
BF059161	IDS	2	297	X	148560303	148560598	PUM2	295	480	2	20493460	20493645
AW138862	TAOK1	1	392	17	27766509	27766899	IDS	391	446	X	148561784	148561839
BU735117	PGAM5	15	223	12	133299111	133299320	IDS	220	380	X	148560838	148560998
CB268858	IDS	3	213	X	148587469	148587686	IDS	213	500	X	148592898	148607295
BX509939	IDS	1	290	X	148560307	148560595	AFMID	276	671	17	76202062	76203316
AA984459	PPM1K	2	55	4	89205095	89205148	IDS	54	409	X	148561256	148561611
CB306816	IDS	17	345	X	148564072	148564400	IDS	343	454	X	148564409	148564520
U66054	IDS	1	187	X	148571843	148577934	LOC100131434	185	425	X	148615706	148626977
BX647783	AFMID	2	644	17	76183443	76203316	IDS	630	925	X	148560300	148560595
AW628693	IDS	4	223	X	148592932	148593151	IDS	222	443	X	148571844	148577970
U66053	LOC100131434	1	302	X	148615706	148626977	IDS	300	487	X	148571843	148577935

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=35)	Stat. for Synonymous SNVs (# total SNVs=17)

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
chr23:148586605-148586605	p.C21C	2
chr23:148564500-148564500	p.S477F	2
chr23:148564557-148564557	p.R458H	2
chr23:148568465-148568465	p.M391V	2
chr23:148585690-148585690	p.A79A	2
chr23:148564645-148564645	p.V429I	2
chr23:148564306-148564306	p.G542R	2
chr23:148571918-148571918	p.V311V	2
chr23:148579685-148579685	p.L221L	2
chr23:148568525-148568525	p.P371A	2

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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	1	5		2	1		3		3			5	1	1			8	4	1	11
# mutation	1	5		2	1		4		3			5	1	1			8	4	1	12
nonsynonymous SNV	1	3		2			3		2			4	1	1			7	3	1	8
synonymous SNV		2			1		1		1			1					1	1		4

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
chrX:148564645	p.V311V,IDS	2
chrX:148571918	p.V429I,IDS	2
chrX:148577945	p.R48C,IDS	1
chrX:148564405	p.V418V,IDS	1
chrX:148584954	p.R271S,IDS	1
chrX:148568501	p.T28R,IDS	1
chrX:148577955	p.T409M,IDS	1
chrX:148564457	p.R271G,IDS	1
chrX:148585690	p.S26C,IDS	1
chrX:148568513	p.S405F,IDS	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 IDS 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 IDS

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


BMPR2,BOD1L1,CREBRF,CHIC1,CHM,IDS,KIAA1109, LEPROT,MECP2,MTM1,MYO5A,PKD2,STAG2,TAF1, TAF1L,TRPC1,TTBK2,WDR44,XIAP,ZNF449,ZNF699	ACAP2,AKT3,BBS7,C16orf52,CA5B,CAMSAP2,CEP120, CHIC1,FAM135A,IDS,KDSR,KRAS,MALT1,MIER1, PAQR3,PCGF5,PJA2,TMEM30A,TRPC1,UBL3,ZDHHC17

AMIGO2,AXL,BICC1,CAV1,CAV2,CDK14,CYP27C1, FRMD6,GATA3,HCG4,IDS,IGFBP3,IGFBP6,LOC100126784, LOXL4,MCC,PDGFC,SEMA7A,TIMP2,TSC22D3,ZNF365	ABCD1,CDIP1,CDC42EP4,CRY2,FOXN3,GABARAPL1,GATSL1, GTF2IP1,HOXC5,IDS,MAOB,MED29,MGC45800,PLA2G4C, RAB11FIP3,SERINC1,SORCS3,STAT6,TBC1D13,TMEM25,TPPP

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 IDS

There's no related Drug.

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Cross referenced IDs for IDS

* 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