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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for UGT2B4 |
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Phenotypic Information for UGT2B4(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: UGT2B4 |
Familial Cancer Database: UGT2B4 |
* 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/ |
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: UGT2B4 |
MedGen: UGT2B4 (Human Medical Genetics with Condition) | |
ClinVar: UGT2B4 | |
Phenotype | MGI: UGT2B4 (International Mouse Phenotyping Consortium) |
PhenomicDB: UGT2B4 |
Mutations for UGT2B4 |
* 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 UGT2B4 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 |
AI114505 | EIF2AK3 | 1 | 169 | 2 | 88922349 | 88922517 | UGT2B4 | 160 | 636 | 4 | 70345883 | 70346360 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
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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=82) | (# total SNVs=35) |
(# total SNVs=0) | (# 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 |
chr4:70359494-70359494 | p.D263N | 3 |
chr4:70359506-70359506 | p.R259* | 3 |
chr4:70346533-70346533 | p.R469H | 3 |
chr4:70355168-70355168 | p.I331V | 3 |
chr4:70361046-70361046 | p.Y178Y | 3 |
chr4:70359471-70359471 | p.L270L | 2 |
chr4:70361195-70361195 | p.D129N | 2 |
chr4:70346495-70346495 | p.D482N | 2 |
chr4:70350946-70350946 | p.K430N | 2 |
chr4:70361460-70361460 | p.K40N | 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 | 3 | 1 | 1 | 8 | 6 |   | 11 |   | 2 |   |   | 22 | 9 | 3 |   |   | 34 | 2 |   | 9 |
# mutation | 3 | 1 | 2 | 8 | 6 |   | 11 |   | 2 |   |   | 25 | 12 | 3 |   |   | 39 | 3 |   | 11 |
nonsynonymous SNV | 2 |   | 1 | 7 | 4 |   | 8 |   |   |   |   | 16 | 9 | 2 |   |   | 28 | 2 |   | 9 |
synonymous SNV | 1 | 1 | 1 | 1 | 2 |   | 3 |   | 2 |   |   | 9 | 3 | 1 |   |   | 11 | 1 |   | 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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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 |
chr4:70346533 | p.R469H,UGT2B4 | 3 |
chr4:70350946 | p.L27L,UGT2B4 | 2 |
chr4:70346553 | p.K430K,UGT2B4 | 2 |
chr4:70361563 | p.D482N,UGT2B4 | 2 |
chr4:70359494 | p.G21G,UGT2B4 | 2 |
chr4:70355231 | p.D263N,UGT2B4 | 2 |
chr4:70361499 | p.F462L,UGT2B4 | 2 |
chr4:70346495 | p.T6I,UGT2B4 | 2 |
chr4:70346374 | p.G522V,UGT2B4 | 2 |
chr4:70361447 | p.E45K,UGT2B4 | 2 |
Other DBs for Point Mutations |
Copy Number for UGT2B4 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 UGT2B4 |
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 |
ARHGEF18,ATRNL1,C12orf60,CCDC85A,ERLIN2,FLJ34503,GABRA1, GABRG2,GDAP1,GPATCH2,KCNK4,MRGPRX2,LINC00176,PCDH19, PEX11G,PRR25,PTPRQ,RD3,UGT2B4,VSIG1,ZNF703 | AGXT,ALDOC,BOK,SPX,CDH20,CDKN2C,DGAT2, ELMOD3,FAM171A2,FGFRL1,GPAM,GPC6,KLB,KRT79, OPRK1,PRRT4,RASGRF2,SPATA9,SSC4D,THRSP,UGT2B4 | ||||
ALOX15B,ANXA13,CIB4,CRISP2,GPR37L1,GSTTP1,GSTTP2, HRASLS5,HSPA2,ICK,ITLN2,KIF19,KLK12,LYZL6, MAK,GRIK1-AS1,OPRD1,RHBDL3,SHISA3,UGT2B4,UMOD | AFM,ALB,APCS,C3P1,C8A,CFHR2,CFHR5, CYP4A22,DNAJB8,F13B,F9,KIR3DP1,KRTAP4-11,KRTAP5-3, LECT2,LOC100129935,LINC00160,OR1N1,SERPINC1,SLC17A2,UGT2B4 |
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 UGT2B4 |
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 |
DB00318 | UDP glucuronosyltransferase 2 family, polypeptide B4 | illicit; approved | Codeine | ||
DB00712 | UDP glucuronosyltransferase 2 family, polypeptide B4 | approved | Flurbiprofen | ||
DB01050 | UDP glucuronosyltransferase 2 family, polypeptide B4 | approved | Ibuprofen | ||
DB01009 | UDP glucuronosyltransferase 2 family, polypeptide B4 | approved | Ketoprofen |
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Cross referenced IDs for UGT2B4 |
* 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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