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 GUSB
Basic gene info.Gene symbolGUSB
Gene nameglucuronidase, beta
SynonymsBG|MPS7
CytomapUCSC genome browser: 7q21.11
Genomic locationchr7 :65425672-65447301
Type of geneprotein-coding
RefGenesNM_000181.3,
NM_001293104.1,NM_001293105.1,NR_120531.1,NM_001284290.1,
Ensembl idENSG00000169919
Descriptionbeta-D-glucuronidasebeta-G1beta-glucuronidase
Modification date20141222
dbXrefs MIM : 611499
HGNC : HGNC
Ensembl : ENSG00000169919
HPRD : 02018
Vega : OTTHUMG00000023735
ProteinUniProt: P08236
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GUSB
BioGPS: 2990
Gene Expression Atlas: ENSG00000169919
The Human Protein Atlas: ENSG00000169919
PathwayNCI Pathway Interaction Database: GUSB
KEGG: GUSB
REACTOME: GUSB
ConsensusPathDB
Pathway Commons: GUSB
MetabolismMetaCyc: GUSB
HUMANCyc: GUSB
RegulationEnsembl's Regulation: ENSG00000169919
miRBase: chr7 :65,425,672-65,447,301
TargetScan: NM_000181
cisRED: ENSG00000169919
ContextiHOP: GUSB
cancer metabolism search in PubMed: GUSB
UCL Cancer Institute: GUSB
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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

check002.gifMetabolic Pathway Description
KEGG_STARCH_AND_SUCROSE_METABOLISM
KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM
KEGG_DRUG_METABOLISM_OTHER_ENZYMES
REACTOME_HYALURONAN_METABOLISM
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM 253220; phenotype.
611499; gene.
Orphanet 584; Mucopolysaccharidosis type 7.
DiseaseKEGG Disease: GUSB
MedGen: GUSB (Human Medical Genetics with Condition)
ClinVar: GUSB
PhenotypeMGI: GUSB (International Mouse Phenotyping Consortium)
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.

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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
breastGUSBchr76543732865437728SGCZchr81426722014267620
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 GUSB related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CV328677GUSB2821676543274565439319CERS5217278125052975450529815

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 # sample11      1     1  
GAIN (# sample)11      1     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=42)
Stat. for Synonymous SNVs
(# total SNVs=12)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr7:65445369-65445369p.P80S3
chr7:65444483-65444483p.F209F2
chr7:65439687-65439687p.R357L2
chr7:65445321-65445321p.V96I2
chr7:65432870-65432870p.L501V2
chr7:65444813-65444813p.P161R2
chr7:65432873-65432873p.C500R2
chr7:65445384-65445384p.V75M2
chr7:65432891-65432891p.P494S1
chr7:65444478-65444478p.Y211S1

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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
# sample1315  2 5  4411 69 5
# mutation1325  2 5  4411 69 6
nonsynonymous SNV1322  1 4  321  28 4
synonymous SNV   3  1 1  12 1 41 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
chr7:65432870p.L355V,GUSB2
chr7:65432873p.C354R,GUSB2
chr7:65432844p.R479T,GUSB1
chr7:65444842p.P295H,GUSB1
chr7:65439597p.A52T,GUSB1
chr7:65425966p.T74T,GUSB1
chr7:65441103p.L456L,GUSB1
chr7:65444845p.M284R,GUSB1
chr7:65439612p.K32K,GUSB1
chr7:65426034p.Q24H,GUSB1

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 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

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

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
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 GUSB
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryChEMBL CHEMBL2728; -.
Organism-specific databasesPharmGKB PA29075; -.
Organism-specific databasesCTD 2990; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB02944glucuronidase, betaexperimentalAlpha-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



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