Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolWBSCR22
Gene nameWilliams Beuren syndrome chromosome region 22
SynonymsHASJ4442|HUSSY-3|MERM1|PP3381|WBMT
CytomapUCSC genome browser: 7q11.23
Genomic locationchr7 :73097897-73112551
Type of geneprotein-coding
RefGenesNM_001202560.2,
NM_017528.4,NR_037776.2,NR_045512.1,
Ensembl idENSG00000262030
DescriptionWilliams-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 date20141207
dbXrefs MIM : 615733
HGNC : HGNC
Ensembl : ENSG00000071462
HPRD : 15659
Vega : OTTHUMG00000023306
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_WBSCR22
BioGPS: 114049
Gene Expression Atlas: ENSG00000262030
The Human Protein Atlas: ENSG00000262030
PathwayNCI Pathway Interaction Database: WBSCR22
KEGG: WBSCR22
REACTOME: WBSCR22
ConsensusPathDB
Pathway Commons: WBSCR22
MetabolismMetaCyc: WBSCR22
HUMANCyc: WBSCR22
RegulationEnsembl's Regulation: ENSG00000262030
miRBase: chr7 :73,097,897-73,112,551
TargetScan: NM_001202560
cisRED: ENSG00000262030
ContextiHOP: WBSCR22
cancer metabolism search in PubMed: WBSCR22
UCL Cancer Institute: WBSCR22
Assigned class in ccmGDBC

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Phenotypic Information for WBSCR22(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_HISTIDINE_METABOLISM
KEGG_TYROSINE_METABOLISM
KEGG_SELENOAMINO_ACID_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: WBSCR22
MedGen: WBSCR22 (Human Medical Genetics with Condition)
ClinVar: WBSCR22
PhenotypeMGI: WBSCR22 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows WBSCR22 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AF251054NDRG322427203528067035374481WBSCR222422258877311237373112538
CK299603ZYX183027143087917143088201WBSCR2229959477309795873101361
BQ188404WBSCR22129577309795973101361ZYX2925797143087917143088204
BF312340SDF413269111641561167358WBSCR2227072677309794073101425
T11661PBX11531164725093164725145WBSCR225317277310770473108355
AW068214WBSCR2287777311225273112321WBSCR227612977311223273112285
DA292433LINC0046116958797671887976786WBSCR226656777311848473134004
BQ375803CCR61541756167484011167484032WBSCR2215847277311018073110494

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample        1        
GAIN (# sample)        1        
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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr7:73108004-73108004p.?2
chr7:73100970-73100970p.R31R2
chr7:73107983-73107983p.S209L2
chr7:73097971-73097971p.R6W1
chr7:73101417-73101417p.G118G1
chr7:73108001-73108001p.?1
chr7:73098102-73098102p.Y18Y1
chr7:73105283-73105283p.K134*1
chr7:73108002-73108002p.?1
chr7:73098116-73098116p.A23V1

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample33 3       321 1 4 4
# mutation33 3       421 1 4 4
nonsynonymous SNV32 2       221   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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr7:73100970p.S209L,WBSCR222
chr7:73107983p.R31R,WBSCR222
chr7:73098102p.M87V,WBSCR221
chr7:73106929p.G274G,WBSCR221
chr7:73112192p.A91S,WBSCR221
chr7:73098116p.R94L,WBSCR221
chr7:73106939p.G103E,WBSCR221
chr7:73098118p.V154V,WBSCR221
chr7:73107716p.R155W,WBSCR221
chr7:73101013p.R158Q,WBSCR221

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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



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