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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for UPP2 |
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Phenotypic Information for UPP2(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: UPP2 |
Familial Cancer Database: UPP2 |
* 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/ |
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KEGG_PYRIMIDINE_METABOLISM KEGG_DRUG_METABOLISM_OTHER_ENZYMES REACTOME_METABOLISM_OF_NUCLEOTIDES REACTOME_PYRIMIDINE_METABOLISM |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: UPP2 |
MedGen: UPP2 (Human Medical Genetics with Condition) | |
ClinVar: UPP2 | |
Phenotype | MGI: UPP2 (International Mouse Phenotyping Consortium) |
PhenomicDB: UPP2 |
Mutations for UPP2 |
* 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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- Statistics for Tissue and Mutation type | Top |
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- For Inter-chromosomal Variations |
There's no inter-chromosomal structural variation. |
- For Intra-chromosomal Variations |
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'. |
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Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | UPP2 | chr2 | 158946037 | 158946057 | UPP2 | chr2 | 158939907 | 158939927 |
pancreas | UPP2 | chr2 | 158950590 | 158950610 | UPP2 | chr2 | 158950824 | 158950844 |
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) |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows UPP2 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 |
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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 |   |   |   | 2 |   |   |   |   |   | 1 |   | 1 | |||
GAIN (# sample) |   |   |   |   |   |   |   |   | 2 |   |   |   |   |   | 1 |   | 1 | |||
LOSS (# sample) |   | 2 |   |   | 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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Stat. for Non-Synonymous SNVs (# total SNVs=24) | (# total SNVs=13) |
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(# total SNVs=4) | (# 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 |
chr2:158962636-158962636 | p.P30S | 3 |
chr2:158971611-158971611 | p.? | 2 |
chr2:158980303-158980303 | p.K238fs*2 | 2 |
chr2:158974332-158974332 | p.? | 2 |
chr2:158971688-158971688 | p.E86K | 2 |
chr2:158980362-158980362 | p.E256K | 2 |
chr2:158991309-158991309 | p.I287I | 2 |
chr2:158977989-158977989 | p.Q175E | 1 |
chr2:158971750-158971750 | p.T106T | 1 |
chr2:158980300-158980300 | p.R235I | 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 | 1 | 1 | 6 | 1 |   | 4 |   | 2 | 1 |   | 12 | 1 |   |   |   | 4 | 5 |   | 6 |
# mutation | 1 | 1 | 1 | 6 | 1 |   | 4 |   | 2 | 1 |   | 14 | 1 |   |   |   | 4 | 6 |   | 6 |
nonsynonymous SNV |   |   | 1 | 2 | 1 |   | 4 |   | 2 |   |   | 10 |   |   |   |   | 4 | 5 |   | 5 |
synonymous SNV | 1 | 1 |   | 4 |   |   |   |   |   | 1 |   | 4 | 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 |
chr2:158971688 | p.V25A,UPP2 | 1 |
chr2:158980394 | p.S120S,UPP2 | 1 |
chr2:158974375 | p.C215C,UPP2 | 1 |
chr2:158958579 | p.G57E,UPP2 | 1 |
chr2:158977989 | p.E127K,UPP2 | 1 |
chr2:158971692 | p.Y220F,UPP2 | 1 |
chr2:158991263 | p.D58H,UPP2 | 1 |
chr2:158974392 | p.L132L,UPP2 | 1 |
chr2:158958584 | p.F233F,UPP2 | 1 |
chr2:158978086 | p.G65S,UPP2 | 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 UPP2 |
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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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BDNF-AS,CLHC1,CCDC146,CCDC148,FGFR3,FLJ40852,GTF2IP1, HSFX2,KLHDC1,LOC202781,LOC644172,LRRC37A3,NDUFA5,GSAP, PKP4,PMS2P4,SEPT7P2,SUGT1P3,UPP2,ZMAT1,ZNF862 | ARHGAP8,ASNS,C12orf76,FAM210B,C20orf96,LINC00240,ERMARD, CFAP53,EFHC1,ELP2,ENOSF1,FBXO15,HAP1,INHA, LOC729375,LRTOMT,OVGP1,PHF21B,SPEF2,UPP2,ZNF433 | ||||
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ARMC2,MRGPRG-AS1,C12orf50,LAMP5,C3orf35,FGF3,FSHR, KLRC3,LRRC36,MSTN,NEK5,NTF4,OOSP2,SACS, SCN2A,SERPINB12,SPANXN2,TM9SF1,TRIM63,UPP2,ZNF117 | ALDH1A2,ARMC4,CCDC144NL,CHRDL2,CNBD1,CST11,DEFB124, DPYS,DYDC1,FAM169B,FCGR3A,FCN3,GLB1L3,GLYCAM1, HAMP,LILRA6,LIM2,LOC55908,MARCO,OR3A4P,PLXNA4, RNASE2,SNORA22, |
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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 UPP2 |
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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 |
DB01101 | uridine phosphorylase 2 | approved; investigational | Capecitabine | ![]() | ![]() |
DB00544 | uridine phosphorylase 2 | approved | Fluorouracil | ![]() | ![]() |
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Cross referenced IDs for UPP2 |
* 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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