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 UROS
Basic gene info.Gene symbolUROS
Gene nameuroporphyrinogen III synthase
SynonymsUROIIIS
CytomapUCSC genome browser: 10q25.2-q26.3
Genomic locationchr10 :127477146-127511837
Type of geneprotein-coding
RefGenesNM_000375.2,
Ensembl idENSG00000188690
Descriptionhydroxymethylbilane hydrolyaseuroporphyrinogen-III cosynthaseuroporphyrinogen-III synthase
Modification date20141219
dbXrefs MIM : 606938
HGNC : HGNC
Ensembl : ENSG00000188690
HPRD : 06087
Vega : OTTHUMG00000019236
ProteinUniProt: P10746
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_UROS
BioGPS: 7390
Gene Expression Atlas: ENSG00000188690
The Human Protein Atlas: ENSG00000188690
PathwayNCI Pathway Interaction Database: UROS
KEGG: UROS
REACTOME: UROS
ConsensusPathDB
Pathway Commons: UROS
MetabolismMetaCyc: UROS
HUMANCyc: UROS
RegulationEnsembl's Regulation: ENSG00000188690
miRBase: chr10 :127,477,146-127,511,837
TargetScan: NM_000375
cisRED: ENSG00000188690
ContextiHOP: UROS
cancer metabolism search in PubMed: UROS
UCL Cancer Institute: UROS
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for UROS(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: UROS
Familial Cancer Database: UROS
* 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_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM
REACTOME_METABOLISM_OF_PORPHYRINS

check002.gifOthers
OMIM 263700; phenotype.
606938; gene.
Orphanet 79277; Congenital erythropoietic porphyria.
DiseaseKEGG Disease: UROS
MedGen: UROS (Human Medical Genetics with Condition)
ClinVar: UROS
PhenotypeMGI: UROS (International Mouse Phenotyping Consortium)
PhenomicDB: UROS

Mutations for UROS
* 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 UROS related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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 # sample1    1  1        
GAIN (# sample)                 
LOSS (# sample)1    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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=13)
Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr10:127486659-127486659p.I150I1
chr10:127504782-127504782p.S37S1
chr10:127477535-127477535p.A234T1
chr10:127486691-127486691p.L140L1
chr10:127504804-127504804p.A30V1
chr10:127477546-127477546p.R230P1
chr10:127486714-127486714p.R132K1
chr10:127505020-127505020p.D17H1
chr10:127477547-127477547p.R230C1
chr10:127495986-127495986p.C130C1

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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
# sample3 14  3     11  12 3
# mutation3 15  3     11  12 3
nonsynonymous SNV2 13  3     11   2 2
synonymous SNV1  2            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
chr10:127503624p.E75Q2
chr10:127477544p.A231T1
chr10:127503639p.D17H1
chr10:127477552p.T228M1
chr10:127503673p.K7Q1
chr10:127483469p.D214N1
chr10:127503692p.A172T1
chr10:127484719p.V167V1
chr10:127504782p.I150I1
chr10:127484732p.L140L1

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 UROS 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 UROS

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

AP2S1,BCCIP,C9orf16,CUEDC2,DHX32,DPCD,ECHS1,
EXOSC1,LHPP,MGMT,MRPL43,MRPL53,MTG1,NDUFB11,
NDUFB8,POLR2H,RNF181,SFXN4,UROS,USMG5,ZNHIT1
AKT1S1,ANAPC11,ATP5I,LAMTOR1,COX6B1,COX8A,HIGD2A,
ISOC2,MRPL20,MRPL36,MRPS11,NDUFA2,NDUFB8,NDUFS8,
PRDX2,PSMB5,PSMD8,TIMM50,UQCR11,UQCRQ,UROS

APOA1BP,ATP5J2,FAM204A,COA6,CCDC58,CMC1,COX7B,
ECE2,FAM96A,GLRX3,LOC440957,MRPL11,MRPL32,MYEOV2,
NDUFB8,PRDX3,RPL26L1,TIMM8B,TOMM22,TRUB1,UROS
COPS3,DRG1,FRG1,GLO1,HAX1,ICT1,LSM10,
MRPL36,MRPS15,MRPS23,NDUFA11,NDUFB8,NSL1,PEX3,
POLR2F,PRDX3,PRKAG1,THOC7,TMEM126A,UROS,VDAC3
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 UROS
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryChEMBL CHEMBL4433; -.
Organism-specific databasesPharmGKB PA37222; -.
Organism-specific databasesCTD 7390; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00145uroporphyrinogen III synthaseapproved; nutraceuticalGlycine


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Cross referenced IDs for UROS
* 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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