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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for NUP62 |
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Phenotypic Information for NUP62(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: NUP62 |
Familial Cancer Database: NUP62 |
* 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/ |
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REACTOME_METABOLISM_OF_NON_CODING_RNA REACTOME_METABOLISM_OF_RNA REACTOME_METABOLISM_OF_CARBOHYDRATES |
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OMIM | 271930; phenotype. 605815; gene. |
Orphanet | 225154; Familial infantile bilateral striatal necrosis. |
Disease | KEGG Disease: NUP62 |
MedGen: NUP62 (Human Medical Genetics with Condition) | |
ClinVar: NUP62 | |
Phenotype | MGI: NUP62 (International Mouse Phenotyping Consortium) |
PhenomicDB: NUP62 |
Mutations for NUP62 |
* 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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There's no structural variation information in COSMIC data for this gene. |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows NUP62 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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There's no copy number variation information in COSMIC data for this gene. |
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Stat. for Non-Synonymous SNVs (# total SNVs=39) | (# total SNVs=12) |
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(# total SNVs=3) | (# total SNVs=2) |
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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 |
chr19:50412217-50412217 | p.S283T | 3 |
chr19:50411525-50411525 | p.E514K | 3 |
chr19:50412728-50412728 | p.G113S | 3 |
chr19:50411509-50411509 | p.I519N | 3 |
chr19:50412417-50412417 | p.S216S | 2 |
chr19:50412045-50412045 | p.W340* | 2 |
chr19:50412230-50412230 | p.A279T | 2 |
chr19:50413058-50413058 | p.G3R | 2 |
chr19:50411513-50411513 | p.R518W | 1 |
chr19:50412893-50412893 | p.G58C | 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 | 2 | 2 | 1 | 5 | 1 |   | 5 |   |   |   |   | 4 | 3 | 1 |   |   | 7 | 7 |   | 6 |
# mutation | 2 | 2 | 2 | 4 | 1 |   | 5 |   |   |   |   | 4 | 3 | 1 |   |   | 7 | 7 |   | 7 |
nonsynonymous SNV | 2 | 2 | 2 | 3 |   |   | 3 |   |   |   |   | 2 | 3 | 1 |   |   | 5 | 3 |   | 4 |
synonymous SNV |   |   |   | 1 | 1 |   | 2 |   |   |   |   | 2 |   |   |   |   | 2 | 4 |   | 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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* 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 |
chr19:50412397 | p.A223V,NUP62 | 2 |
chr19:50413062 | p.M1I,NUP62 | 2 |
chr19:50411536 | p.I477I,NUP62 | 1 |
chr19:50412682 | p.A318T,NUP62 | 1 |
chr19:50411880 | p.A94S,NUP62 | 1 |
chr19:50412220 | p.T460T,NUP62 | 1 |
chr19:50411625 | p.G317G,NUP62 | 1 |
chr19:50412728 | p.S89F,NUP62 | 1 |
chr19:50411934 | p.L458V,NUP62 | 1 |
chr19:50412396 | p.V310V,NUP62 | 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 NUP62 |
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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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AKT1S1,AP2A1,BCL2L12,C19orf48,CD3EAP,CNOT3,KIF18B, LIG1,MED25,NUP62,POLD1,PPP5C,PRMT1,SAE1, PPP6R1,SCAF1,TRIM28,TSEN34,U2AF2,ZNF473,ZNF71 | ASB6,CHERP,DHX37,EHMT2,H2AFY2,INTS5,CCAR2, KRBA1,MCM5,MYBBP1A,NOP2,NUP62,POLD1,SEPT9, SLC12A9,SMARCA4,TCF3,TRAF2,ZBTB12,ZNF48,ZNF74 |
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CCDC97,CNOT3,FIZ1,GRWD1,HNRNPUL1,LIG1,MGC2752, NUP62,PRPF31,PRR12,SAE1,SCAF1,TRIM28,U2AF2, ZBTB45,ZNF324,ZNF324B,ZNF45,ZNF526,ZNF574,ZSCAN22 | DHX30,DUSP7,ELAC2,HAUS5,IMPDH1,IPO9,L3MBTL2, MDC1,MSH6,NUP188,NUP62,PARP1,PELP1,PHF19, R3HDM1,TCHP,TCOF1,TTC26,TXLNA,UBAP2L,UBFD1 |
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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 NUP62 |
There's no related Drug. |
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Cross referenced IDs for NUP62 |
* 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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