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 GUSB

Basic gene info.	Gene symbol	GUSB
	Gene name	glucuronidase, beta
	Synonyms	BG\|MPS7
	Cytomap	UCSC genome browser: 7q21.11
	Genomic location	chr7 :65425672-65447301
	Type of gene	protein-coding
	RefGenes	NM_000181.3, NM_001293104.1,NM_001293105.1,NR_120531.1,NM_001284290.1,
	Ensembl id	ENSG00000169919
	Description	beta-D-glucuronidasebeta-G1beta-glucuronidase
	Modification date	20141222
dbXrefs	MIM : 611499
	HGNC : HGNC
	Ensembl : ENSG00000169919
	HPRD : 02018
	Vega : OTTHUMG00000023735
Protein	UniProt: P08236 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GUSB
	BioGPS: 2990
	Gene Expression Atlas: ENSG00000169919
	The Human Protein Atlas: ENSG00000169919
Pathway	NCI Pathway Interaction Database: GUSB
	KEGG: GUSB
	REACTOME: GUSB
	ConsensusPathDB
	Pathway Commons: GUSB
Metabolism	MetaCyc: GUSB
	HUMANCyc: GUSB
Regulation	Ensembl's Regulation: ENSG00000169919
	miRBase: chr7 :65,425,672-65,447,301
	TargetScan: NM_000181
	cisRED: ENSG00000169919
Context	iHOP: GUSB
	cancer metabolism search in PubMed: GUSB
	UCL Cancer Institute: GUSB
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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

Cancer Description
Cancer	CGAP: GUSB
	Familial Cancer Database: GUSB

* 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 KIRC ⁶,	Therapeutic Vulnerabilities in Cancer⁷

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,
6 http://www.nature.com/nature/journal/v499/n7456/full/nature12222.html,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
KEGG_STARCH_AND_SUCROSE_METABOLISM KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM KEGG_DRUG_METABOLISM_OTHER_ENZYMES REACTOME_HYALURONAN_METABOLISM REACTOME_METABOLISM_OF_CARBOHYDRATES

Others
OMIM	253220; phenotype. 611499; gene.
Orphanet	584; Mucopolysaccharidosis type 7.
Disease	KEGG Disease: GUSB
	MedGen: GUSB (Human Medical Genetics with Condition)
	ClinVar: GUSB
Phenotype	MGI: GUSB (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GUSB

Mutations for GUSB

* 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

There's no intra-chromosomal structural variation.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
breast	GUSB	chr7	65437328	65437728	SGCZ	chr8	14267220	14267620

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 GUSB related fusion information.

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

CV328677

GUSB

216

65432745

65439319

CERS5

217

278

50529754

50529815

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=42)	Stat. for Synonymous SNVs (# total SNVs=12)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=1)

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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
chr7:65445369-65445369	p.P80S	3
chr7:65444813-65444813	p.P161R	2
chr7:65432873-65432873	p.C500R	2
chr7:65445384-65445384	p.V75M	2
chr7:65444483-65444483	p.F209F	2
chr7:65439687-65439687	p.R357L	2
chr7:65445321-65445321	p.V96I	2
chr7:65432870-65432870	p.L501V	2
chr7:65439577-65439577	p.Q394*	1
chr7:65445324-65445324	p.F95V	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	1	3	1	5			2		5			4	4	1	1		6	9		5
# mutation	1	3	2	5			2		5			4	4	1	1		6	9		6
nonsynonymous SNV	1	3	2	2			1		4			3	2	1			2	8		4
synonymous SNV				3			1		1			1	2		1		4	1		2

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
chr7:65432870	p.L355V,GUSB	2
chr7:65432873	p.C354R,GUSB	2
chr7:65440036	p.P452L,GUSB	1
chr7:65432837	p.V256A,GUSB	1
chr7:65444795	p.L24L,GUSB	1
chr7:65447157	p.L425L,GUSB	1
chr7:65439419	p.Y242C,GUSB	1
chr7:65441055	p.Y21C,GUSB	1
chr7:65432838	p.F403C,GUSB	1
chr7:65444796	p.P241L,GUSB	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 GUSB 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 GUSB

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


AACS,ACSBG1,ACSM1,AKR1D1,B3GAT1,C6orf223,FCN2, GSTM5,GSTT2,GUSB,LOC91948,LST-3TM12,MAGEB3,MYOM2, NANOG,NOTO,PNLIPRP3,RLN3,RNASE11,RNASE12,TMPRSS9	ADAM2,ALOX15B,APOD,DHRS2,ENPP3,GGT1,GUSB, HAAO,HIST1H4H,IDI1,NANOG,NAT2,PLA2G4E,PPEF1, RNASE12,SERHL2,SERHL,SPINK8,SULT1C3,UGT2B10,UGT2B11

AGXT,APBA1,LRRC75B,CYP1B1-AS1,CAPN9,CASD1,FAM83E, FRZB,GATAD1,GUSB,KLK3,PDE9A,RAP1GAP,RNASE4, SPINK4,STYXL1,TFF3,TSPAN13,WNK4,WNT4,XBP1	ACVR1B,ADCY6,ATF6B,CANT1,CLMN,CMTM4,GALNT12, GRHL2,GTF3C2,GUSB,ILDR1,LIMK2,MCTP2,NEU4, PPFIBP2,SEMA4G,SLC26A6,SMPDL3B,TOX3,WRNIP1,ZBTB42

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 GUSB

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	ChEMBL	CHEMBL2728; -.
Organism-specific databases	PharmGKB	PA29075; -.
Organism-specific databases	CTD	2990; -.

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
DB02944	glucuronidase, beta	experimental	Alpha-D-Mannose

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Cross referenced IDs for GUSB

* 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