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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SNUPN |
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Phenotypic Information for SNUPN(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: SNUPN |
Familial Cancer Database: SNUPN |
* 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_NON_CODING_RNA REACTOME_METABOLISM_OF_RNA |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: SNUPN |
MedGen: SNUPN (Human Medical Genetics with Condition) | |
ClinVar: SNUPN | |
Phenotype | MGI: SNUPN (International Mouse Phenotyping Consortium) |
PhenomicDB: SNUPN |
Mutations for SNUPN |
* 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 SNUPN 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 |
BC007306 | SNUPN | 1473 | 1497 | 15 | 75918632 | 75918656 | ATIC | 1489 | 3397 | 2 | 216176838 | 216214479 |
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=23) | (# total SNVs=4) |
(# total SNVs=1) | (# 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 |
chr15:75901910-75901910 | p.S164* | 2 |
chr15:75901916-75901916 | p.R162Q | 2 |
chr15:75902239-75902239 | p.A134S | 2 |
chr15:75902273-75902273 | p.V122V | 2 |
chr15:75909787-75909787 | p.D89N | 1 |
chr15:75890848-75890848 | p.H312D | 1 |
chr15:75899623-75899623 | p.E178D | 1 |
chr15:75909831-75909831 | p.E74G | 1 |
chr15:75890860-75890860 | p.Q308K | 1 |
chr15:75909889-75909889 | p.R55W | 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 |   | 4 |   |   |   |   |   |   |   | 3 |   | 1 |   |   | 5 | 3 |   | 6 |
# mutation |   | 1 |   | 4 |   |   |   |   |   |   |   | 3 |   | 1 |   |   | 5 | 3 |   | 6 |
nonsynonymous SNV |   | 1 |   | 3 |   |   |   |   |   |   |   | 2 |   | 1 |   |   | 3 | 2 |   | 4 |
synonymous SNV |   |   |   | 1 |   |   |   |   |   |   |   | 1 |   |   |   |   | 2 | 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 |
chr15:75902273 | p.R162Q,SNUPN | 2 |
chr15:75901916 | p.V122V,SNUPN | 2 |
chr15:75901981 | p.E220K,SNUPN | 1 |
chr15:75890848 | p.Q200H,SNUPN | 1 |
chr15:75902272 | p.S140S,SNUPN | 1 |
chr15:75890927 | p.V123M,SNUPN | 1 |
chr15:75890955 | p.H353R,SNUPN | 1 |
chr15:75902304 | p.P112L,SNUPN | 1 |
chr15:75890977 | p.S348S,SNUPN | 1 |
chr15:75909787 | p.D89N,SNUPN | 1 |
Other DBs for Point Mutations |
Copy Number for SNUPN 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 SNUPN |
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 |
C15orf40,C15orf61,CLK3,CLN6,COMMD4,COX5A,FBXO22, FBXO22-AS1,IMP3,MRPL46,MRPS11,MTHFS,PPCDC,PSMA4, RPL4,RPLP1,RPS17,SNUPN,ST20,UBL7,WDR61 | C16orf13,ELP6,COX4I1,CUEDC2,EDF1,NAA38,MED11, MRPL11,MRPL18,MRPL43,MRPL52,MRPS21,NDUFA11,POLD2, SF3B5,SNUPN,TCEB2,TIMM22,TXN2,UBL7,ZNF511 |
ADPGK,VWA9,C15orf61,FAM103A1,FAM96A,FBXO22,IMP3, MRPL46,PSMA4,PTPLAD1,RCN2,RPL4,RPLP1,RPS17, RSL24D1,SNUPN,SPG21,EMC4,UBL7,WDR61,ZFAND6 | ADH5,BOLA1,C18orf21,COMMD3,GEMIN6,GPX1,HSCB, HTRA2,MRPL40,MRPS14,NENF,NFU1,NUDCD2,OST4, POP7,PTPMT1,RPS13,SNRPD2,SNUPN,TATDN3,THYN1 |
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 SNUPN |
There's no related Drug. |
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Cross referenced IDs for SNUPN |
* 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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