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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for UPF3B |
Basic gene info. | Gene symbol | UPF3B |
Gene name | UPF3 regulator of nonsense transcripts homolog B (yeast) | |
Synonyms | HUPF3B|MRX62|MRXS14|RENT3B|UPF3X | |
Cytomap | UCSC genome browser: Xq24 | |
Genomic location | chrX :118967988-118986991 | |
Type of gene | protein-coding | |
RefGenes | NM_023010.3, NM_080632.2, | |
Ensembl id | ENSG00000125351 | |
Description | hUpf3p-Xmental retardation, X-linked 62nonsense mRNA reducing factor 3Bregulator of nonsense transcripts 3Bup-frameshift suppressor 3 homolog Bup-frameshift suppressor 3 homolog on chromosome X | |
Modification date | 20141219 | |
dbXrefs | MIM : 300298 | |
HGNC : HGNC | ||
Ensembl : ENSG00000125351 | ||
HPRD : 02247 | ||
Vega : OTTHUMG00000022282 | ||
Protein | UniProt: Q9BZI7 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_UPF3B | |
BioGPS: 65109 | ||
Gene Expression Atlas: ENSG00000125351 | ||
The Human Protein Atlas: ENSG00000125351 | ||
Pathway | NCI Pathway Interaction Database: UPF3B | |
KEGG: UPF3B | ||
REACTOME: UPF3B | ||
ConsensusPathDB | ||
Pathway Commons: UPF3B | ||
Metabolism | MetaCyc: UPF3B | |
HUMANCyc: UPF3B | ||
Regulation | Ensembl's Regulation: ENSG00000125351 | |
miRBase: chrX :118,967,988-118,986,991 | ||
TargetScan: NM_023010 | ||
cisRED: ENSG00000125351 | ||
Context | iHOP: UPF3B | |
cancer metabolism search in PubMed: UPF3B | ||
UCL Cancer Institute: UPF3B | ||
Assigned class in ccmGDB | B - This gene belongs to cancer gene. |
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Phenotypic Information for UPF3B(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: UPF3B |
Familial Cancer Database: UPF3B |
* 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 | |
REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA |
Others | |
OMIM | 300298; gene. 300676; phenotype. |
Orphanet | 323; FG syndrome. 776; X-linked intellectual disability with marfanoid habitus. 777; X-linked non-syndromic intellectual disability. |
Disease | KEGG Disease: UPF3B |
MedGen: UPF3B (Human Medical Genetics with Condition) | |
ClinVar: UPF3B | |
Phenotype | MGI: UPF3B (International Mouse Phenotyping Consortium) |
PhenomicDB: UPF3B |
Mutations for UPF3B |
* 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 UPF3B 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 |
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=66) | (# total SNVs=10) |
(# total SNVs=2) | (# 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 |
chr23:118971920-118971920 | p.R368W | 7 |
chr23:118972431-118972431 | p.K302N | 2 |
chr23:118971941-118971941 | p.R361* | 2 |
chr23:118968882-118968882 | p.E471K | 2 |
chr23:118971992-118971992 | p.D344H | 2 |
chr23:118972357-118972357 | p.S327N | 2 |
chr23:118971919-118971919 | p.R368Q | 2 |
chr23:118972370-118972370 | p.K323* | 2 |
chr23:118977163-118977163 | p.E191K | 1 |
chr23:118986793-118986793 | p.S33R | 1 |
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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 | 5 | 1 | 6 |   |   | 1 |   | 1 |   |   | 5 | 5 |   |   |   | 6 | 3 |   | 15 |
# mutation | 1 | 5 | 1 | 5 |   |   | 1 |   | 1 |   |   | 6 | 6 |   |   |   | 6 | 3 |   | 19 |
nonsynonymous SNV | 1 | 4 | 1 | 3 |   |   |   |   | 1 |   |   | 5 | 5 |   |   |   | 5 | 2 |   | 17 |
synonymous SNV |   | 1 |   | 2 |   |   | 1 |   |   |   |   | 1 | 1 |   |   |   | 1 | 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 |
chrX:118971919 | p.E458K,UPF3B | 2 |
chrX:118968882 | p.R355L,UPF3B | 2 |
chrX:118986832 | p.E191K,UPF3B | 1 |
chrX:118972448 | p.P75L,UPF3B | 1 |
chrX:118977174 | p.R348Q,UPF3B | 1 |
chrX:118985490 | p.N189T,UPF3B | 1 |
chrX:118971887 | p.H70Y,UPF3B | 1 |
chrX:118986836 | p.P324T,UPF3B | 1 |
chrX:118974609 | p.A187V,UPF3B | 1 |
chrX:118977197 | p.K47R,UPF3B | 1 |
Other DBs for Point Mutations |
Copy Number for UPF3B 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 UPF3B |
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 |
CCDC77,CDC25A,CDCA3,CDCA7,CDCA8,FAM136A,FAM64A, FOXM1,KIF2C,MAGOH,NASP,NKRF,ORC1,PRPF38A, PSRC1,RAD54L,RCC2,SERBP1,STMN1,TMSB15B,UPF3B | ACIN1,R3HCC1L,CCDC174,C9orf173,NSRP1,CIR1,CLK2, CWC25,PNN,PRPF3,RBM6,RSRC2,SLTM,TTF1, UPF2,UPF3B,ZC3H8,ZNF23,ZNF343,ZNF740,ZSCAN21 |
BRCC3,DKC1,HDAC8,HMGB3,HNRNPH2,HTATSF1,LAS1L, MORF4L2,NKAP,NKRF,NONO,PHF6,RBMX2,SLC25A14, THOC2,TIMM8A,TSR2,UPF3B,UTP14A,VMA21,ZNF280C | CHTOP,CCAR1,CWC27,DNAJC10,EIF5B,HAUS6,LUC7L2, LUC7L3,ME1,METTL3,NEDD1,PAPPA2,PARP2,PPIG, PRMT9,PRPF38B,RBM17,SENP1,SRSF11,SREK1,UPF3B |
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 UPF3B |
There's no related Drug. |
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Cross referenced IDs for UPF3B |
* 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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