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 WBSCR17
Basic gene info.Gene symbolWBSCR17
Gene nameWilliams-Beuren syndrome chromosome region 17
SynonymsGALNACT17|GALNT16|GALNT20|GALNTL3|GalNAc-T5L
CytomapUCSC genome browser: 7q11.23
Genomic locationchr7 :70597788-71178584
Type of geneprotein-coding
RefGenesNM_022479.2,
Ensembl idENSG00000185274
DescriptionUDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase-like 3UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase-like protein 3UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 16galNAc-T-like protein 3polypeptide
Modification date20141207
dbXrefs MIM : 615137
HGNC : HGNC
Ensembl : ENSG00000185274
HPRD : 15655
Vega : OTTHUMG00000129783
ProteinUniProt: Q6IS24
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_WBSCR17
BioGPS: 64409
Gene Expression Atlas: ENSG00000185274
The Human Protein Atlas: ENSG00000185274
PathwayNCI Pathway Interaction Database: WBSCR17
KEGG: WBSCR17
REACTOME: WBSCR17
ConsensusPathDB
Pathway Commons: WBSCR17
MetabolismMetaCyc: WBSCR17
HUMANCyc: WBSCR17
RegulationEnsembl's Regulation: ENSG00000185274
miRBase: chr7 :70,597,788-71,178,584
TargetScan: NM_022479
cisRED: ENSG00000185274
ContextiHOP: WBSCR17
cancer metabolism search in PubMed: WBSCR17
UCL Cancer Institute: WBSCR17
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for WBSCR17(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: WBSCR17
Familial Cancer Database: WBSCR17
* 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 COAD 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/v487/n7407/full/nature11252.html,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: WBSCR17
MedGen: WBSCR17 (Human Medical Genetics with Condition)
ClinVar: WBSCR17
PhenotypeMGI: WBSCR17 (International Mouse Phenotyping Consortium)
PhenomicDB: WBSCR17

Mutations for WBSCR17
* 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

- Statistics for Tissue and Mutation typeTop
- 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
* 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
large_intestineWBSCR17chr77081589770815897CALN1chr77138580171385801
ovaryWBSCR17chr77069990070699920chr77046472670464746
ovaryWBSCR17chr77071097370710993AUTS2chr77006581570065835
ovaryWBSCR17chr77085869470858714WBSCR17chr77090886770908887
ovaryWBSCR17chr77092325370923273NLGN4Xchr2359865145986534
ovaryWBSCR17chr77092325670923276WBSCR17chr77092368770923707
ovaryWBSCR17chr77092367270923692NLGN4Xchr2359868325986852
ovaryWBSCR17chr77098189670981916WBSCR17chr77098366870983688
ovaryWBSCR17chr77107447471074494chr78803581888035838
pancreasWBSCR17chr77060872470608744WBSCR17chr77060878970608809
pancreasWBSCR17chr77083240070832420WBSCR17chr77083282070832840
pancreasWBSCR17chr77087568770875707chr76563338465633404
pancreasWBSCR17chr77090743670907456PIONchr77697804676978066
pancreasWBSCR17chr77098735670987376WBSCR17chr77098741470987434
pancreasWBSCR17chr77106584071065860chr2387158158715835
pancreasWBSCR17chr77108017171080191DLDchr7107553881107553901
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows WBSCR17 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA178830SLC39A11170177094989570949964WBSCR176751477113039471175771
BI001777WBSCR17128177117766271177943WBSCR1728056777117724871177534
S60878INPP4B8344143719085143719135WBSCR17153577089778670897806

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 # sample16 4  3 4 2  2  1
GAIN (# sample)15 3  3 4 2  2  1
LOSS (# sample) 1 1             
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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=177)		Stat. for Synonymous SNVs
(# total SNVs=57)
Stat. for Deletions
(# total SNVs=1)		Stat. for Insertions
(# total SNVs=0)
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
chr7:70853279-70853279p.V161M4
chr7:70800611-70800611p.P105L4
chr7:71036319-71036319p.G338S4
chr7:70800577-70800577p.R94W4
chr7:70885994-70885994p.E289K4
chr7:70853312-70853312p.V172M3
chr7:70800608-70800608p.S104F3
chr7:70800709-70800709p.R138C3
chr7:71134961-71134961p.P424L3
chr7:71036364-71036364p.E353Q3

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample35 359 8 61 30142 14823 14
# mutation35 349 8 71 29162 14823 18
nonsynonymous SNV34 307 6 51 24101 13019 14
synonymous SNV 1 52 2 2  561  184 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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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
chr7:70800709p.E433E3
chr7:70885988p.A175A3
chr7:71134989p.R138C3
chr7:70800611p.R287W3
chr7:70885994p.P105L3
chr7:70853323p.E289K3
chr7:71142235p.R334R2
chr7:71130575p.F337F2
chr7:70885902p.G482R2
chr7:71177028p.D312N2

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 WBSCR17 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 WBSCR17

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

ACAN,CAPN2,CSPG4,EXTL1,FAM19A3,HCN1,JPH2,
KCNG1,MFGE8,OR11H4,PADI2,PGM5P2,PMP2,PTPN14,
RLBP1,SLC15A1,SOX6,SPINT4,TRPV4,WBSCR17,ZBTB32		CD276,CERCAM,CNPY4,COL1A1,COL1A2,COL3A1,COL5A1,
COL6A2,EMILIN2,ISLR,KCNB2,MRC2,NGF,OAF,
PCOLCE,PRRX2,RCN3,SPON2,THY1,WBSCR17,WNT2

ATP1A2,GNAO1,HAND2,HSPB8,KANK2,KCNMB1,LMOD1,
LONRF2,MAB21L2,MYH11,MYLK,MYOCD,NECAB1,PDZRN4,
POPDC2,PPP1R12B,RASL12,RGMA,SCN7A,SYNM,WBSCR17		ARHGAP6,C20orf194,CAP2,COPZ2,DENND5A,FBXL2,GNAZ,
JAZF1,KIAA1462,LOC100128239,MAP6,HAND2-AS1,PBX3,RILPL1,
SCN7A,STX2,TMOD1,TTC7B,TUBG2,WBSCR17,ZBTB47
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 WBSCR17


There's no related Drug.
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Cross referenced IDs for WBSCR17
* 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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