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 UXS1
Basic gene info.Gene symbolUXS1
Gene nameUDP-glucuronate decarboxylase 1
SynonymsSDR6E1|UGD
CytomapUCSC genome browser: 2q12.2
Genomic locationchr2 :106709758-106810795
Type of geneprotein-coding
RefGenesNM_001253875.1,
NM_001253876.1,NM_025076.4,NR_045607.1,
Ensembl idENSG00000115652
DescriptionUDP-glucuronic acid decarboxylase 1UXS-1short chain dehydrogenase/reductase family 6E, member 12
Modification date20141209
dbXrefs MIM : 609749
HGNC : HGNC
Ensembl : ENSG00000115652
HPRD : 15642
Vega : OTTHUMG00000153150
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_UXS1
BioGPS: 80146
Gene Expression Atlas: ENSG00000115652
The Human Protein Atlas: ENSG00000115652
PathwayNCI Pathway Interaction Database: UXS1
KEGG: UXS1
REACTOME: UXS1
ConsensusPathDB
Pathway Commons: UXS1
MetabolismMetaCyc: UXS1
HUMANCyc: UXS1
RegulationEnsembl's Regulation: ENSG00000115652
miRBase: chr2 :106,709,758-106,810,795
TargetScan: NM_001253875
cisRED: ENSG00000115652
ContextiHOP: UXS1
cancer metabolism search in PubMed: UXS1
UCL Cancer Institute: UXS1
Assigned class in ccmGDBC

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Phenotypic Information for UXS1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: UXS1
Familial Cancer Database: UXS1
* 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_STARCH_AND_SUCROSE_METABOLISM
KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: UXS1
MedGen: UXS1 (Human Medical Genetics with Condition)
ClinVar: UXS1
PhenotypeMGI: UXS1 (International Mouse Phenotyping Consortium)
PhenomicDB: UXS1

Mutations for UXS1
* 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
There's no inter-chromosomal structural variation.
- 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
ovaryUXS1chr2106739958106740158SH3RF3chr2109991610109991810
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 UXS1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE156057UXS1241332106710595106713264PCBP2131543125385451553854927
BF367966UXS123012106710218106710518VTI1A29847110114374416114374589

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   1    2   1  
GAIN (# sample)     1    2   1  
LOSS (# sample) 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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=44)
Stat. for Synonymous SNVs
(# total SNVs=4)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=2)
There's no deleted 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
chr2:106761805-106761805p.V105L2
chr2:106761696-106761696p.E141G2
chr2:106721281-106721281p.G298W1
chr2:106739476-106739476p.D237Y1
chr2:106761704-106761704p.I138I1
chr2:106715192-106715192p.Q341R1
chr2:106721286-106721286p.G296E1
chr2:106761814-106761814p.A102T1
chr2:106739478-106739478p.Y236C1
chr2:106761713-106761713p.E135D1

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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
# sample 21102 1 3 1542  33 6
# mutation 21112 1 3 1541  33 6
nonsynonymous SNV 21102 1 2  441  23 5
synonymous SNV   1    1 11    1  1
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
chr2:106761805p.V105L,UXS12
chr2:106761768p.F104F,UXS11
chr2:106715192p.L144I,UXS11
chr2:106739433p.T15A,UXS11
chr2:106761696p.P4S,UXS11
chr2:106761798p.R95I,UXS11
chr2:106715213p.V142V,UXS11
chr2:106739451p.D149D,UXS11
chr2:106761704p.E69K,UXS11
chr2:106717534p.L137V,UXS11

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 UXS1 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 UXS1

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

AADACL3,ACTR3,BIN1,BUB1,CCDC138,DDX18,EIF5B,
ERCC3,IL22RA2,IWS1,MAP4K4,NIFK,MRPS9,NCK2,
POLR1B,POLR2D,R3HDML,SAP130,TMEM177,TTL,UXS1
AIMP2,AKR1B1,ATP5G1,CCDC167,MSANTD3,GTF3C6,HCFC1R1,
HN1,HSPA8,MRPL14,OAZ2,ORAI1,PDLIM2,PDXP,
PKM,RNF34,SLC16A3,SLC35B1,SLC35E4,STARD7,UXS1

ATIC,CCDC115,CIAO1,LGALSL,LOC654342,LRP11,METTL5,
MTX2,PCYOX1,PDCL3,PRKRA,RDH14,RNF149,SF3B14,
SLC19A3,SMYD5,SSB,TPRKB,UNC50,UXS1,WDSUB1
ERICH5,CLDN8,CPA6,FAM3D,HEPACAM2,IFT57,IGSF22,
IL1R2,LOC284578,MFSD4,PRAC1,RNF2,SAMD13,SLC35A1,
SLPI,SPAG16,STARD10,TMEM38A,UXS1,VSIG2,ZG16
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 UXS1


There's no related Drug.
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Cross referenced IDs for UXS1
* 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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