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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for UGT1A4 |
Basic gene info. | Gene symbol | UGT1A4 |
Gene name | UDP glucuronosyltransferase 1 family, polypeptide A4 | |
Synonyms | HUG-BR2|UDPGT|UDPGT 1-4|UGT-1D|UGT1-04|UGT1.4|UGT1D | |
Cytomap | UCSC genome browser: 2q37 | |
Genomic location | chr2 :234627437-234681945 | |
Type of gene | protein-coding | |
RefGenes | NM_007120.2, | |
Ensembl id | ENSG00000244474 | |
Description | UDP glycosyltransferase 1 family, polypeptide A4UDP-glucuronosyltransferase 1-4UDP-glucuronosyltransferase 1-DUDP-glucuronosyltransferase 1A4bilirubin UDP-glucuronosyltransferase isozyme 2bilirubin-specific UDPGT isozyme 2 | |
Modification date | 20141211 | |
dbXrefs | MIM : 606429 | |
HGNC : HGNC | ||
Ensembl : ENSG00000244474 | ||
HPRD : 08402 | ||
Vega : OTTHUMG00000059119 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_UGT1A4 | |
BioGPS: 54657 | ||
Gene Expression Atlas: ENSG00000244474 | ||
The Human Protein Atlas: ENSG00000244474 | ||
Pathway | NCI Pathway Interaction Database: UGT1A4 | |
KEGG: UGT1A4 | ||
REACTOME: UGT1A4 | ||
ConsensusPathDB | ||
Pathway Commons: UGT1A4 | ||
Metabolism | MetaCyc: UGT1A4 | |
HUMANCyc: UGT1A4 | ||
Regulation | Ensembl's Regulation: ENSG00000244474 | |
miRBase: chr2 :234,627,437-234,681,945 | ||
TargetScan: NM_007120 | ||
cisRED: ENSG00000244474 | ||
Context | iHOP: UGT1A4 | |
cancer metabolism search in PubMed: UGT1A4 | ||
UCL Cancer Institute: UGT1A4 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for UGT1A4(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: UGT1A4 |
Familial Cancer Database: UGT1A4 |
* This gene is included in those cancer gene databases. |
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/ |
Metabolic Pathway Description | |
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM KEGG_STARCH_AND_SUCROSE_METABOLISM KEGG_RETINOL_METABOLISM KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450 KEGG_DRUG_METABOLISM_CYTOCHROME_P450 KEGG_DRUG_METABOLISM_OTHER_ENZYMES |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: UGT1A4 |
MedGen: UGT1A4 (Human Medical Genetics with Condition) | |
ClinVar: UGT1A4 | |
Phenotype | MGI: UGT1A4 (International Mouse Phenotyping Consortium) |
PhenomicDB: UGT1A4 |
Mutations for UGT1A4 |
* 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows UGT1A4 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 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   | |||
GAIN (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=51) | (# total SNVs=19) |
(# total SNVs=3) | (# total SNVs=1) |
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Top 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 position | Mutation(aa) | Unique sampleID count |
chr2:234681161-234681161 | p.K521E | 3 |
chr2:234676526-234676526 | p.S344L | 3 |
chr2:234627914-234627914 | p.L150L | 3 |
chr2:234627592-234627592 | p.L42L | 2 |
chr2:234677057-234677057 | p.A427T | 2 |
chr2:234681146-234681146 | p.R516W | 2 |
chr2:234676494-234676494 | p.? | 2 |
chr2:234681041-234681041 | p.D481N | 2 |
chr2:234680936-234680936 | p.S446G | 2 |
chr2:234628143-234628143 | p.T226I | 2 |
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SNV Counts per Each Loci in TCGA data |
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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 | 2 | 2 | 6 | 1 |   | 1 |   | 2 |   |   | 4 | 1 | 2 |   |   | 12 | 3 |   | 3 |
# mutation | 1 | 2 | 2 | 6 | 1 |   | 1 |   | 2 |   |   | 5 | 1 | 2 |   |   | 11 | 3 |   | 3 |
nonsynonymous SNV | 1 | 2 | 2 | 6 |   |   |   |   | 2 |   |   | 2 | 1 | 1 |   |   | 6 | 2 |   | 3 |
synonymous SNV |   |   |   |   | 1 |   | 1 |   |   |   |   | 3 |   | 1 |   |   | 5 | 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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Top 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 Position | Mutation(aa) | Unique sampleID count |
chr2:234627728 | p.E88K | 2 |
chr2:234627587 | p.A58A | 1 |
chr2:234628292 | p.M205T | 1 |
chr2:234627926 | p.M205I | 1 |
chr2:234628116 | p.V92I | 1 |
chr2:234627598 | p.R210R | 1 |
chr2:234628294 | p.S111Y | 1 |
chr2:234627950 | p.P217H | 1 |
chr2:234628118 | p.A123A | 1 |
chr2:234627599 | p.L218V | 1 |
Other DBs for Point Mutations |
Copy Number for UGT1A4 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 UGT1A4 |
Gene 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. |
Differential 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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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-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 |
APCS,APOA2,APOA4,APOC3,C8A,C9,CREB3L3, CRP,F2,FABP1,FGF23,GDF2,HP,ITIH1, MT1B,PLG,SERPINA7,SLC17A2,SULT2A1,TM4SF5,UGT1A4 | BRS3,CDX2,DKFZp686A1627,DSCR8,GOLGA6L6,KRTAP9-8,LOC348021, MAGEB2,NR1H4,OR4F4,OR4K15,OR5B17,OR5D16,OR5J2, POTEB,URAD,PYDC1,SEBOX,SLC22A6,UGT1A4,XAGE2 | ||||
ABCG2,ALPI,C11orf86,LINC00520,C1orf94,CAPN11,CIDEC, CLDN23,DHRS9,FAM25BP,GDPD2,GLRA4,LOC646627,MYPN, NAT8,TRANK1,UGT1A1,UGT1A3,UGT1A4,UGT1A5,VSIG1 | ABCC2,ABCG5,ALDOB,APOB,CEACAM20,CYP3A4,DAB1, DPEP1,FABP6,FGF19,GSTA2,HAPLN4,MGAM,NAT8, NTS,RBP2,SLC10A2,SLC2A2,SLC34A3,SLC5A12,UGT1A4 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for UGT1A4 |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00252 | UDP glucuronosyltransferase 1 family, polypeptide A4 | approved | Phenytoin | ||
DB00683 | UDP glucuronosyltransferase 1 family, polypeptide A4 | illicit; approved | Midazolam | ||
DB00184 | UDP glucuronosyltransferase 1 family, polypeptide A4 | approved | Nicotine | ||
DB03255 | UDP glucuronosyltransferase 1 family, polypeptide A4 | experimental | Phenol | ||
DB00675 | UDP glucuronosyltransferase 1 family, polypeptide A4 | approved | Tamoxifen | ||
DB00762 | UDP glucuronosyltransferase 1 family, polypeptide A4 | approved; investigational | Irinotecan | ||
DB00477 | UDP glucuronosyltransferase 1 family, polypeptide A4 | approved | Chlorpromazine | ||
DB00363 | UDP glucuronosyltransferase 1 family, polypeptide A4 | approved | Clozapine | ||
DB00458 | UDP glucuronosyltransferase 1 family, polypeptide A4 | approved | Imipramine | ||
DB00555 | UDP glucuronosyltransferase 1 family, polypeptide A4 | approved; investigational | Lamotrigine | ||
DB00454 | UDP glucuronosyltransferase 1 family, polypeptide A4 | approved | Meperidine | ||
DB00334 | UDP glucuronosyltransferase 1 family, polypeptide A4 | approved; investigational | Olanzapine |
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Cross referenced IDs for UGT1A4 |
* 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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