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 WBSCR22

Basic gene info.	Gene symbol	WBSCR22
	Gene name	Williams Beuren syndrome chromosome region 22
	Synonyms	HASJ4442\|HUSSY-3\|MERM1\|PP3381\|WBMT
	Cytomap	UCSC genome browser: 7q11.23
	Genomic location	chr7 :73097897-73112551
	Type of gene	protein-coding
	RefGenes	NM_001202560.2, NM_017528.4,NR_037776.2,NR_045512.1,
	Ensembl id	ENSG00000262030
	Description	Williams-Beuren candidate region putative methyltransferaseWilliams-Beuren syndrome chromosomal region 22 proteinbud site selection protein 23 homologmetastasis-related methyltransferase 1probable 18S rRNA (guanine-N(7))-methyltransferaseribosome bio
	Modification date	20141207
dbXrefs	MIM : 615733
	HGNC : HGNC
	Ensembl : ENSG00000071462
	HPRD : 15659
	Vega : OTTHUMG00000023306
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_WBSCR22
	BioGPS: 114049
	Gene Expression Atlas: ENSG00000262030
	The Human Protein Atlas: ENSG00000262030
Pathway	NCI Pathway Interaction Database: WBSCR22
	KEGG: WBSCR22
	REACTOME: WBSCR22
	ConsensusPathDB
	Pathway Commons: WBSCR22
Metabolism	MetaCyc: WBSCR22
	HUMANCyc: WBSCR22
Regulation	Ensembl's Regulation: ENSG00000262030
	miRBase: chr7 :73,097,897-73,112,551
	TargetScan: NM_001202560
	cisRED: ENSG00000262030
Context	iHOP: WBSCR22
	cancer metabolism search in PubMed: WBSCR22
	UCL Cancer Institute: WBSCR22
Assigned class in ccmGDB	C

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Phenotypic Information for WBSCR22(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: WBSCR22
	Familial Cancer Database: WBSCR22

* 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_HISTIDINE_METABOLISM KEGG_TYROSINE_METABOLISM KEGG_SELENOAMINO_ACID_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: WBSCR22
	MedGen: WBSCR22 (Human Medical Genetics with Condition)
	ClinVar: WBSCR22
Phenotype	MGI: WBSCR22 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: WBSCR22

Mutations for WBSCR22

* 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 WBSCR22 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
AF251054	NDRG3	2	2427	20	35280670	35374481	WBSCR22	2422	2588	7	73112373	73112538
CK299603	ZYX	18	302	7	143087917	143088201	WBSCR22	299	594	7	73097958	73101361
BQ188404	WBSCR22	1	295	7	73097959	73101361	ZYX	292	579	7	143087917	143088204
BF312340	SDF4	13	269	1	1164156	1167358	WBSCR22	270	726	7	73097940	73101425
T11661	PBX1	1	53	1	164725093	164725145	WBSCR22	53	172	7	73107704	73108355
AW068214	WBSCR22	8	77	7	73112252	73112321	WBSCR22	76	129	7	73112232	73112285
DA292433	LINC00461	1	69	5	87976718	87976786	WBSCR22	66	567	7	73118484	73134004
BQ375803	CCR6	154	175	6	167484011	167484032	WBSCR22	158	472	7	73110180	73110494

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=15)	Stat. for Synonymous SNVs (# total SNVs=4)

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
chr7:73107983-73107983	p.S209L	2
chr7:73108004-73108004	p.?	2
chr7:73100970-73100970	p.R31R	2
chr7:73111966-73111966	p.V245M	1
chr7:73101226-73101226	p.M87I	1
chr7:73107963-73107963	p.L202L	1
chr7:73111988-73111988	p.V252G	1
chr7:73101334-73101334	p.A91S	1
chr7:73112020-73112020	p.G263S	1
chr7:73101344-73101344	p.R94L	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	3	3		3								3	2	1		1		4		4
# mutation	3	3		3								4	2	1		1		4		4
nonsynonymous SNV	3	2		2								2	2	1				4		2
synonymous SNV		1		1								2				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
chr7:73100970	p.S209L,WBSCR22	2
chr7:73107983	p.R31R,WBSCR22	2
chr7:73101334	p.G103E,WBSCR22	1
chr7:73111952	p.V154V,WBSCR22	1
chr7:73101344	p.R155W,WBSCR22	1
chr7:73111966	p.R158Q,WBSCR22	1
chr7:73101371	p.D190Y,WBSCR22	1
chr7:73112015	p.S209S,WBSCR22	1
chr7:73106928	p.Y18Y,WBSCR22	1
chr7:73112020	p.E214Q,WBSCR22	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 WBSCR22 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 WBSCR22

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


ALKBH4,ARF5,ATP5J2,ATP6V1F,BCL7B,BUD31,COPS6, DGUOK,DNAJC30,NDUFA1,NDUFB2,NSUN5,PDAP1,POLR2J, POP7,SHFM1,SSBP1,TMUB1,WBSCR16,WBSCR22,ZNHIT1	COA4,CHMP6,LSM4,MRPL52,MRPS12,NHP2,NSUN5, PFDN6,PMF1,POLR2F,POP7,PPP1CA,PPP2R1A,PSMD13, PUF60,RNF187,SGTA,TIMM17B,TMED1,TMEM134,WBSCR22

ALKBH4,ARF5,BUD31,PPP1R35,C7orf50,LAMTOR4,COPS6, CPSF4,DNAJC30,GNB2,MDH2,MRPS24,NSUN5,PDAP1, POLR2J,POP7,SHFM1,TMUB1,WBSCR16,WBSCR22,ZNHIT1	APTX,BNIP1,BOLA3,HYPK,EBNA1BP2,MRPL3,MRTO4, NHP2,NHP2L1,NME2,NPM3,NR2C2AP,PHB,POLR1C, PRDX4,RAN,SNRPB,SNRPE,TMEM147,TOMM6,WBSCR22

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 WBSCR22

There's no related Drug.

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Cross referenced IDs for WBSCR22

* 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