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 GNS

Basic gene info.	Gene symbol	GNS
	Gene name	glucosamine (N-acetyl)-6-sulfatase
	Synonyms	G6S
	Cytomap	UCSC genome browser: 12q14
	Genomic location	chr12 :65107221-65153226
	Type of gene	protein-coding
	RefGenes	NM_002076.3,
	Ensembl id	ENSG00000135677
	Description	N-acetylglucosamine-6-sulfataseglucosamine-6-sulfatase
	Modification date	20141207
dbXrefs	MIM : 607664
	HGNC : HGNC
	Ensembl : ENSG00000135677
	HPRD : 09637
	Vega : OTTHUMG00000168819
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GNS
	BioGPS: 2799
	Gene Expression Atlas: ENSG00000135677
	The Human Protein Atlas: ENSG00000135677
Pathway	NCI Pathway Interaction Database: GNS
	KEGG: GNS
	REACTOME: GNS
	ConsensusPathDB
	Pathway Commons: GNS
Metabolism	MetaCyc: GNS
	HUMANCyc: GNS
Regulation	Ensembl's Regulation: ENSG00000135677
	miRBase: chr12 :65,107,221-65,153,226
	TargetScan: NM_002076
	cisRED: ENSG00000135677
Context	iHOP: GNS
	cancer metabolism search in PubMed: GNS
	UCL Cancer Institute: GNS
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: GNS
	Familial Cancer Database: GNS

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

Mutations for GNS

* 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

There's no inter-chromosomal structural variation.

- 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	GNS	chr12	65127061	65127081		chr12	64625672	64625692

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 GNS 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
CR741239	NPHP3-ACAD11	1	188	3	132400417	132400604	GNS	184	494	12	65108727	65109037
AI701812	AKAP9	1	186	7	91719457	91719642	GNS	186	416	12	65107421	65107650
N40382	OPTN	1	95	10	13160997	13164435	GNS	94	439	12	65108698	65109037
BQ434418	CAND1	18	312	12	67696101	67696395	GNS	311	529	12	65115383	65116895
DB469756	ZNF691	1	373	1	43312254	43316740	GNS	368	453	12	65108835	65108920
CA449339	GNS	18	453	12	65107229	65107664	NCAM2	448	732	21	22558984	22559273
BE708454	GNS	1	339	12	65138036	65138375	ESRP1	331	496	8	95718809	95718977

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=36)	Stat. for Synonymous SNVs (# total SNVs=8)

Stat. for Deletions (# total SNVs=2)	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
chr12:65137006-65137006	p.S236L	2
chr12:65115486-65115486	p.?	2
chr12:65146499-65146499	p.M77I	2
chr12:65130842-65130842	p.D347V	2
chr12:65137060-65137060	p.Y218C	2
chr12:65134422-65134422	p.S280Y	2
chr12:65113959-65113959	p.F475L	1
chr12:65141500-65141500	p.L151V	1
chr12:65130789-65130789	p.S365R	1
chr12:65110563-65110563	p.R539R	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=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	3	2	1	6			2		1			1	2				2	4		8
# mutation	3	2	1	8			2		1			1	2				2	4		8
nonsynonymous SNV	2		1	7			1		1				1				2	3		5
synonymous SNV	1	2		1			1					1	1					1		3

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
chr12:65134422	p.S280Y	2
chr12:65115435	p.R539C	1
chr12:65133254	p.S365R	1
chr12:65110564	p.G527R	1
chr12:65115466	p.Q363E	1
chr12:65133264	p.P526P	1
chr12:65110565	p.P351P	1
chr12:65115473	p.R506R	1
chr12:65113803	p.P351S	1
chr12:65116805	p.R506W	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 GNS 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 GNS

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


AFF4,APC,APOOL,C12orf66,CANX,CCNT1,CHM, FNIP1,GNS,LEMD3,LMBRD2,MON2,PLBD2,RAPGEF6, RASSF3,SERINC3,SERINC5,SLC25A46,TBK1,TTC37,UEVLD	ANGPT1,ARHGAP21,ASAH1,ASPH,BHMT2,CHRDL1,DENND5A, ECM2,EPB41L2,GLP2R,GNG2,GNS,ITGB1,ITSN1, KLHL5,LAMA4,RHOQ,SEPT11,SORBS1,STS,ZDHHC3

C3AR1,CSF1,CSF1R,CTSB,GIT2,GNS,LAPTM5, LRRC25,MAFB,MNDA,MYO5A,NRP1,PDCD1LG2,PLBD2, PLXNC1,PSAP,PTAFR,RAB8B,SSH1,TLR1,TSHZ2	ABCD1,AHCYL1,APC,ATRN,CREB3L2,EXOC6B,GNS, LONP2,MAOB,NBAS,NUCB1,OSR2,PI4K2A,PLOD1, SEC31A,SIRPA,SLC9A6,SMC3,TMEM25,TPP1,UBE2R2

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 GNS

There's no related Drug.

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Cross referenced IDs for GNS

* 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