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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for UROD |
Basic gene info. | Gene symbol | UROD |
Gene name | uroporphyrinogen decarboxylase | |
Synonyms | PCT|UPD | |
Cytomap | UCSC genome browser: 1p34 | |
Genomic location | chr1 :45477804-45481341 | |
Type of gene | protein-coding | |
RefGenes | NM_000374.4, NR_036510.1, | |
Ensembl id | ENSG00000126088 | |
Description | uroporphyrinogen III decarboxylase | |
Modification date | 20141219 | |
dbXrefs | MIM : 613521 | |
HGNC : HGNC | ||
Ensembl : ENSG00000126088 | ||
HPRD : 01441 | ||
Vega : OTTHUMG00000008949 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_UROD | |
BioGPS: 7389 | ||
Gene Expression Atlas: ENSG00000126088 | ||
The Human Protein Atlas: ENSG00000126088 | ||
Pathway | NCI Pathway Interaction Database: UROD | |
KEGG: UROD | ||
REACTOME: UROD | ||
ConsensusPathDB | ||
Pathway Commons: UROD | ||
Metabolism | MetaCyc: UROD | |
HUMANCyc: UROD | ||
Regulation | Ensembl's Regulation: ENSG00000126088 | |
miRBase: chr1 :45,477,804-45,481,341 | ||
TargetScan: NM_000374 | ||
cisRED: ENSG00000126088 | ||
Context | iHOP: UROD | |
cancer metabolism search in PubMed: UROD | ||
UCL Cancer Institute: UROD | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for UROD(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: UROD |
Familial Cancer Database: UROD |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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/ |
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KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM REACTOME_METABOLISM_OF_PORPHYRINS |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: UROD |
MedGen: UROD (Human Medical Genetics with Condition) | |
ClinVar: UROD | |
Phenotype | MGI: UROD (International Mouse Phenotyping Consortium) |
PhenomicDB: UROD |
Mutations for UROD |
* 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. |
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There's no structural variation information in COSMIC data for this gene. |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows UROD related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
BU157543 | NSRP1 | 184 | 209 | 17 | 28503625 | 28503653 | UROD | 210 | 646 | 1 | 45478873 | 45479740 | |
AA368910 | UROD | 1 | 204 | 1 | 45481049 | 45481492 | UROD | 194 | 335 | 1 | 45479387 | 45479642 | |
AW385230 | UROD | 1 | 65 | 1 | 45480445 | 45480509 | MCM3AP-AS1 | 61 | 483 | 21 | 47654247 | 47654670 | |
BE772547 | HIPK1 | 1 | 319 | 1 | 114515938 | 114516256 | UROD | 316 | 530 | 1 | 45480619 | 45481163 | |
BE772548 | HIPK1 | 4 | 338 | 1 | 114515938 | 114516275 | UROD | 335 | 557 | 1 | 45480619 | 45481171 | |
BM718816 | LMO4 | 17 | 156 | 1 | 87810949 | 87811091 | UROD | 149 | 220 | 1 | 45481176 | 45481247 |
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There's no copy number variation information in COSMIC data for this gene. |
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Stat. for Non-Synonymous SNVs (# total SNVs=13) | (# total SNVs=7) |
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(# total SNVs=0) | (# total SNVs=1) |
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* 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 position | Mutation(aa) | Unique sampleID count |
chr1:45477941-45477941 | p.E2K | 2 |
chr1:45479709-45479709 | p.P201P | 2 |
chr1:45479683-45479683 | p.R193C | 1 |
chr1:45480657-45480658 | p.C308fs*7 | 1 |
chr1:45479706-45479706 | p.V200V | 1 |
chr1:45481012-45481012 | p.E316K | 1 |
chr1:45477952-45477952 | p.G5G | 1 |
chr1:45481027-45481027 | p.V321M | 1 |
chr1:45478626-45478626 | p.A23V | 1 |
chr1:45480122-45480122 | p.L216L | 1 |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 1 |   |   | 4 |   |   | 3 |   | 2 | 1 |   |   | 1 | 2 |   |   | 1 | 1 |   | 1 |
# mutation | 1 |   |   | 4 |   |   | 3 |   | 2 | 1 |   |   | 1 | 2 |   |   | 1 | 1 |   | 1 |
nonsynonymous SNV |   |   |   | 2 |   |   | 1 |   | 1 | 1 |   |   | 1 | 1 |   |   |   | 1 |   | 1 |
synonymous SNV | 1 |   |   | 2 |   |   | 2 |   | 1 |   |   |   |   | 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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* 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 Position | Mutation(aa) | Unique sampleID count |
chr1:45480182 | p.Q302H | 1 |
chr1:45477952 | p.V321M | 1 |
chr1:45480410 | p.M345V | 1 |
chr1:45478626 | p.R365Q | 1 |
chr1:45480612 | p.G5G | 1 |
chr1:45478653 | p.A23V | 1 |
chr1:45480642 | p.P32L | 1 |
chr1:45478860 | p.P62P | 1 |
chr1:45481027 | p.I82I | 1 |
chr1:45478996 | p.R122Q | 1 |
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* 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. |
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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 UROD |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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 |
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ARL6IP4,AURKAIP1,B4GALT7,C19orf70,C1orf122,C1orf123,C1orf86, PRADC1,LAMTOR4,DMAP1,DPM3,ERI3,GADD45GIP1,LSM10, NDUFA13,NDUFB7,NDUFS7,THAP3,UROD,ZNF593,ZNHIT1 | ABHD14A,ANXA11,ARL2,BLOC1S1,BLVRB,LAMTOR1,CCDC23, CCM2,CD63,GPX1,GPX4,HINT2,LRP3,MYL6, NEDD8,NUCB1,POLR2L,PSMD8,RNPEPL1,SNX17,UROD | ||||
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ADPRHL2,AKR1A1,ATP6V0B,BLOC1S1,C1orf123,SMIM12,ECI1, DGCR6L,LSM10,NAA38,PEF1,POLR2L,PSMB10,PSMB6, PSME1,SCO2,SRA1,STX8,TRAPPC3,TRNAU1AP,UROD | ANAPC16,ARL2,BOLA1,BRK1,CCDC23,DCTN3,FBXL5, FIS1,FUNDC2,MANBAL,MRPL40,PFDN1,RWDD2B,SNAPIN, SNX3,THTPA,TPD52L2,UROD,YPEL5,ZMAT5,ZNF32 |
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* 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 |
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Pharmacological Information for UROD |
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DB Category | DB Name | DB's ID and Url link |
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* Gene Centered Interaction Network. |
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* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00145 | uroporphyrinogen decarboxylase | approved; nutraceutical | Glycine | ![]() | ![]() |
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Cross referenced IDs for UROD |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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