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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for UPF2 |
Basic gene info. | Gene symbol | UPF2 |
Gene name | UPF2 regulator of nonsense transcripts homolog (yeast) | |
Synonyms | HUPF2|RENT2|smg-3 | |
Cytomap | UCSC genome browser: 10p14-p13 | |
Genomic location | chr10 :11962020-12085169 | |
Type of gene | protein-coding | |
RefGenes | NM_015542.3, NM_080599.2, | |
Ensembl id | ENSG00000151461 | |
Description | nonsense mRNA reducing factor 2regulator of nonsense transcripts 2smg-3 homolog, nonsense mediated mRNA decay factorup-frameshift suppressor 2 homologyeast Upf2p homolog | |
Modification date | 20141207 | |
dbXrefs | MIM : 605529 | |
HGNC : HGNC | ||
Ensembl : ENSG00000151461 | ||
HPRD : 10405 | ||
Vega : OTTHUMG00000017678 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_UPF2 | |
BioGPS: 26019 | ||
Gene Expression Atlas: ENSG00000151461 | ||
The Human Protein Atlas: ENSG00000151461 | ||
Pathway | NCI Pathway Interaction Database: UPF2 | |
KEGG: UPF2 | ||
REACTOME: UPF2 | ||
ConsensusPathDB | ||
Pathway Commons: UPF2 | ||
Metabolism | MetaCyc: UPF2 | |
HUMANCyc: UPF2 | ||
Regulation | Ensembl's Regulation: ENSG00000151461 | |
miRBase: chr10 :11,962,020-12,085,169 | ||
TargetScan: NM_015542 | ||
cisRED: ENSG00000151461 | ||
Context | iHOP: UPF2 | |
cancer metabolism search in PubMed: UPF2 | ||
UCL Cancer Institute: UPF2 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for UPF2(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: UPF2 |
Familial Cancer Database: UPF2 |
* 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 | |
Orphanet | |
Disease | KEGG Disease: UPF2 |
MedGen: UPF2 (Human Medical Genetics with Condition) | |
ClinVar: UPF2 | |
Phenotype | MGI: UPF2 (International Mouse Phenotyping Consortium) |
PhenomicDB: UPF2 |
Mutations for UPF2 |
* 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 |
- Statistics for Tissue and Mutation type | Top |
- For Inter-chromosomal Variations |
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'. |
- For Intra-chromosomal Variations |
There's no intra-chromosomal structural variation. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | UPF2 | chr10 | 11969783 | 11969803 | CAMK1D | chr10 | 12648556 | 12648576 |
ovary | UPF2 | chr10 | 11977024 | 11977044 | chr6 | 91633241 | 91633261 | |
ovary | UPF2 | chr10 | 11986422 | 11986442 | UPF2 | chr10 | 11986494 | 11986514 |
ovary | UPF2 | chr10 | 12003668 | 12003688 | LOC219731 | chr10 | 11903175 | 11903195 |
pancreas | UPF2 | chr10 | 12002482 | 12002502 | chr10 | 16005765 | 16005785 |
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows UPF2 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 |
BU570216 | ENY2 | 4 | 370 | 8 | 110346561 | 110352793 | UPF2 | 361 | 479 | 10 | 12077064 | 12077182 | |
DA212995 | MIR100HG | 1 | 262 | 11 | 121972154 | 121972413 | UPF2 | 260 | 481 | 10 | 12046668 | 12056185 | |
BQ438570 | ENY2 | 4 | 370 | 8 | 110346561 | 110352793 | UPF2 | 361 | 479 | 10 | 12077064 | 12077182 | |
CD639413 | USP32 | 1 | 209 | 17 | 58407704 | 58407912 | UPF2 | 210 | 499 | 10 | 12071405 | 12077228 | |
BU567506 | ENY2 | 4 | 370 | 8 | 110346561 | 110352793 | UPF2 | 361 | 478 | 10 | 12077065 | 12077182 | |
BU570150 | ENY2 | 4 | 370 | 8 | 110346561 | 110352793 | UPF2 | 361 | 479 | 10 | 12077064 | 12077182 | |
BG385736 | USP6NL | 2 | 262 | 10 | 11639628 | 11653614 | UPF2 | 262 | 464 | 10 | 11998317 | 11998520 | |
CR738223 | UPF2 | 1 | 61 | 10 | 12011461 | 12011521 | MTAP | 55 | 220 | 9 | 21861026 | 21861193 | |
BI054523 | UPF2 | 11 | 70 | 10 | 12071117 | 12071176 | GLUD1 | 59 | 141 | 10 | 88811189 | 88811305 |
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 | 2 | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
GAIN (# sample) | 2 | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
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=96) | (# total SNVs=30) |
(# total SNVs=2) | (# total SNVs=0) |
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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 |
chr10:11990443-11990443 | p.E1033D | 9 |
chr10:12077417-12077417 | p.P2P | 4 |
chr10:11990494-11990494 | p.D1016D | 4 |
chr10:12009405-12009405 | p.R668C | 3 |
chr10:12070800-12070800 | p.L363F | 3 |
chr10:12077380-12077380 | p.D15Y | 2 |
chr10:12021104-12021104 | p.D635D | 2 |
chr10:12071456-12071456 | p.R145C | 2 |
chr10:12043687-12043687 | p.L548I | 2 |
chr10:12056056-12056056 | p.P425A | 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 | 3 | 1 | 20 | 1 |   | 5 |   | 6 |   |   | 6 | 5 | 2 |   |   | 16 | 10 |   | 12 |
# mutation | 3 | 3 | 1 | 22 | 1 |   | 6 |   | 7 |   |   | 8 | 5 | 2 |   |   | 17 | 11 |   | 15 |
nonsynonymous SNV | 2 | 2 | 1 | 18 | 1 |   | 4 |   | 5 |   |   | 6 | 4 | 2 |   |   | 11 | 9 |   | 12 |
synonymous SNV | 1 | 1 |   | 4 |   |   | 2 |   | 2 |   |   | 2 | 1 |   |   |   | 6 | 2 |   | 3 |
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 |
chr10:11990443 | p.E1033D,UPF2 | 7 |
chr10:12009405 | p.R668C,UPF2 | 3 |
chr10:12070784 | p.R369G,UPF2 | 2 |
chr10:12039698 | p.R606L,UPF2 | 2 |
chr10:11994167 | p.K103N,UPF2 | 1 |
chr10:12039755 | p.Q1229H,UPF2 | 1 |
chr10:12077195 | p.E994K,UPF2 | 1 |
chr10:11971960 | p.L771L,UPF2 | 1 |
chr10:12001176 | p.A637T,UPF2 | 1 |
chr10:12070767 | p.E92K,UPF2 | 1 |
Other DBs for Point Mutations |
Copy Number for UPF2 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 UPF2 |
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 |
ARL5B,CDC123,CWC22,DCLRE1C,DHTKD1,GDI2,GTPBP4, HSPA14,KIN,MASTL,MCM10,MLLT10,NUDT5,PRPF18, RBM17,SEC61A2,SEPHS1,STAM,SUV39H2,UPF2,USP6NL | CASP8AP2,EPC1,KDM5A,ICE1,KRIT1,MGA,NFX1, NIPBL,PIK3C3,RABGAP1,RBM41,RNF169,RSF1,SETD2, SHPRH,SMC3,THOC2,TPR,UPF2,ZNF197,ZNF791 |
ALMS1,BIRC6,BMS1,FAM208B,EPC1,FBXO18,GOLGA4, HEATR5B,INO80,LARP4B,MDN1,RBBP6,RBM17,SLTM, SMC3,TAF3,UPF2,USP34,WAC,ZNF37A,ZNF638 | BAZ1B,BOD1L1,DOCK9,EIF5B,HTATSF1,LYST,MDC1, MYCBP2,PBRM1,RBM26,ROCK1,SNTB2,SRRM1,SUPT16H, SUPT6H,TANC1,UBAP2L,UPF2,YTHDC1,ZC3H13,ZNF37A |
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 UPF2 |
There's no related Drug. |
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Cross referenced IDs for UPF2 |
* 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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